Variable valve apparatus and methods

ABSTRACT

Sample processing devices with variable valve structures and methods of using the same are disclosed. The valve structures allow for removal of selected portions of the sample material located within the process chamber. Removal of the selected portions is achieved by forming an opening in a valve septum at a desired location. The valve septums may be large enough to allow for adjustment of the location of the opening based on the characteristics of the sample material in the process chamber. If the sample processing device is rotated after the opening is formed, the selected portion of the material located closer to the axis of rotation exits the process chamber through the opening. The remainder of the sample material cannot exit through the opening because it is located farther from the axis of rotation than the opening.

CROSS-REFERENCE TO RELATED APPLICATIONS

The present application is a Continuation-In-Part of U.S. patentapplication Ser. No. 10/734,717, filed on Dec. 12, 2003, and claimspriority to U.S. Provisional Patent Application Ser. No. 60/532,523,filed on Dec. 24, 2003, both of which are incorporated herein byreference in their entireties.

BACKGROUND

Sample processing devices including process chambers in which variouschemical or biological processes are performed play an increasing rolein scientific and/or diagnostic investigations. The process chambersprovided in such devices are preferably small in volume to reduce theamount of sample material required to perform the processes.

One persistent issue associated with sample processing devices includingprocess chambers is in the transfer of fluids between different featuresin the devices. Conventional approaches to separate and transfer fluidiccontents of process chambers have often required human intervention(e.g., manual pipetting) and/or robotic manipulation. Such transferprocesses suffer from a number of disadvantages including, but notlimited to, the potential for errors, complexity and associated highcosts, etc.

Attempts to address the fluid transfer issues have focused ontransferring the entire fluid contents of the process chambers through,e.g., valves, tortuous paths, etc.

SUMMARY OF THE INVENTION

The present invention provides sample processing devices with valvestructures. The valve structures allow for removal of selected portionsof the sample material located within the process chamber. Removal ofthe selected portions is achieved by forming an opening in a valveseptum at a desired location.

The valve septums are preferably large enough to allow for adjustment ofthe location of the opening based on the characteristics of the samplematerial in the process chamber. If the sample processing device isrotated after the opening is formed, the selected portion of thematerial located closer to the axis of rotation exits the processchamber through the opening. The remainder of the sample material cannotexit through the opening because it is located farther from the axis ofrotation than the opening.

The openings in the valve septum may be formed at locations based on oneor more characteristics of the sample material detected within theprocess chamber. It may be preferred that the process chambers includedetection windows that transmit light into and/or out of the processchamber. Detected characteristics of the sample material may include,e.g., the free surface of the sample material (indicative of the volumeof sample material in the process chamber). Forming an opening in thevalve septum at a selected distance radially outward of the free surfacecan provide the ability to remove a selected volume of the samplematerial from the process chamber.

For sample materials that can be separated into various components,e.g., whole blood, rotation of the sample processing device may resultin separation of the plasma and red blood cell components, thus allowingfor selective removal of the components to, e.g., different processchambers.

In some embodiments, it may be possible to remove selected aliquots ofthe sample material by forming openings at selected locations in one ormore valve septums. The selected aliquot volume can be determined basedon the radial distance between the openings (measured relative to theaxis of rotation) and the cross-sectional area of the process chamberbetween the opening.

The openings in the valve septums are preferably formed in the absenceof physical contact, e.g., through laser ablation, focused opticalheating, etc. As a result, the openings can preferably be formed withoutpiercing the outermost layers of the sample processing device, thuslimiting the possibility of leakage of the sample material from thesample processing device.

In one aspect, the present invention provides a valved process chamberon a sample processing device, the valved process chamber including aprocess chamber having a process chamber volume located between opposingfirst and second major sides of the sample processing device, whereinthe process chamber occupies a process chamber area on the sampleprocessing device, and wherein the process chamber area has a length anda width transverse to the length, and further wherein the length isgreater than the width. The valved process chamber also includes a valvechamber located within the process chamber area, the valve chamberlocated between the process chamber volume and the second major side ofthe sample processing device, wherein the valve chamber is isolated fromthe process chamber by a valve septum separating the valve chamber andthe process chamber, and wherein a portion of the process chamber volumelies between the valve septum and a first major side of the sampleprocessing device. A detection window is located within the processchamber area, wherein the detection window is transmissive to selectedelectromagnetic energy directed into and/or out of the process chambervolume.

In another aspect, the present invention provides a valved processchamber on a sample processing device, the valved process chamberincluding a process chamber having a process chamber volume locatedbetween opposing first and second major sides of the sample processingdevice, wherein the process chamber occupies a process chamber area onthe sample processing device, and wherein the process chamber area has alength and a width transverse to the length, and further wherein thelength is greater than the width. The valved process chamber alsoincludes a valve chamber located within the process chamber area, thevalve chamber located between the process chamber volume and the secondmajor side of the sample processing device, wherein the valve chamber isisolated from the process chamber by a valve septum separating the valvechamber and the process chamber, and wherein a portion of the processchamber volume lies between the valve septum and a first major side ofthe sample processing device, and further wherein the valve chamber andthe detection window occupy mutually exclusive portions of the processchamber area, and still further wherein at least a portion of the valvechamber is located within a valve lip extending into the process chamberarea, and wherein the valve septum is formed in the valve lip. Adetection window is located within the process chamber area, wherein thedetection window is transmissive to selected electromagnetic energydirected into and/or out of the process chamber volume.

In another aspect, the present invention includes a method ofselectively removing sample material from a process chamber. The methodincludes providing a sample processing device that includes a processchamber having a process chamber volume, wherein the process chamberoccupies a process chamber area on the sample processing device; a valvechamber located within the process chamber area, wherein the valvechamber is isolated from the process chamber by a valve septum locatedbetween the valve chamber and the process chamber; and a detectionwindow located within the process chamber area, wherein the detectionwindow is transmissive for selected electromagnetic energy. The methodfurther includes providing sample material in the process chamber;detecting a characteristic of the sample material in the process chamberthrough the detection window; and forming an opening in the valve septumat a selected location along the length of the process chamber, whereinthe selected location is correlated to the detected characteristic ofthe sample material. The method also includes moving only a portion ofthe sample material from the process chamber into the valve chamberthrough the opening formed in the valve septum.

In another aspect, the present invention provides a method ofselectively removing sample material from a process chamber. The methodincludes providing a sample processing device having a process chamberwith a process chamber volume, wherein the process chamber occupies aprocess chamber area on the sample processing device, and wherein theprocess chamber area includes a length and a width transverse to thelength, and further wherein the length is greater than the width. Thesample processing device also includes a valve chamber located withinthe process chamber area, wherein the valve chamber is isolated from theprocess chamber by a valve septum located between the valve chamber andthe process chamber; and a detection window located within the processchamber area, wherein the detection window is transmissive for selectedelectromagnetic energy. The method also includes providing samplematerial in the process chamber; detecting a characteristic of thesample material in the process chamber through the detection window;forming an opening in the valve septum at a selected location within theprocess chamber area, wherein the selected location is correlated to thedetected characteristic of the sample material; and moving only aportion of the sample material from the process chamber into the valvechamber through the opening formed in the valve septum by rotating thesample processing device.

In another embodiment, the present invention provides a method ofisolating nucleic acid from whole blood, the method including: providinga device that includes a loading chamber and a variable valved processchamber; placing whole blood in the loading chamber; transferring thewhole blood to a valved process chamber; centrifuging the whole blood inthe valved process chamber to form a plasma layer (often the upperlayer), a red blood cell layer (often the lower layer), and aninterfacial layer that includes white blood cells; removing at least aportion of the interfacial layer; and lysing the white blood cells inthe separated interfacial layer and optionally lysing the nuclei thereinto release inhibitors and/or nucleic acid.

If desired, prior to lysing the white blood cells, the method caninclude diluting the separated interfacial layer of the sample withwater (preferably, RNAse-free sterile water) or buffer, optionallyfurther concentrating the diluted layer to increase the concentration ofnucleic acid material, optionally separating the further concentratedregion, and optionally repeating this process of dilution followed byconcentration and separation to reduce the inhibitor concentration tothat which would not interfere with an amplification method.

Alternatively, before, simultaneously with, or after lysing the whiteblood cells, if desired, the method can include transferring theseparated interfacial layer to a separation chamber for contact withsolid phase material to preferentially adhere at least a portion of theinhibitors to the solid phase material; wherein the solid phase materialincludes capture sites (e.g., chelating functional groups), a coatingreagent coated on the solid phase material, or both; wherein the coatingreagent is selected from the group consisting of a surfactant, a strongbase, a polyelectrolyte, a selectively permeable polymeric barrier, andcombinations thereof.

Another embodiment of the present invention involves a method ofisolating nucleic acid from whole blood using a density gradientmaterial. In this embodiment, the method includes: providing a devicethat includes a loading chamber and a variable valved process chamber;placing whole blood in the loading chamber; transferring the whole bloodto a valved process chamber; contacting the whole blood with a densitygradient material; centrifuging the whole blood and density gradientmaterial in the valved process chamber to form layers, at least one ofwhich contains cells of interest; removing at least a portion of thelayer that includes the cells of interest; and lysing the separatedcells of interest to release nucleic acid.

In another embodiment, the present invention provides a method ofisolating nucleic acid from whole blood that includes a pathogen, themethod includes: providing a device that includes a loading chamber, avariable valved process chamber, and a separation chamber with pathogencapture material therein; placing whole blood in the loading chamber;transferring the whole blood to a valved process chamber; centrifugingthe whole blood in the valved process chamber to form a plasma layerthat includes a pathogen, a red blood cell layer, and an interfaciallayer that includes white blood cells; transferring at least a portionof the plasma layer with the pathogen to the separation chamberincluding pathogen capture material; separating at least a portion ofthe pathogen from the pathogen capture material; and lysing the pathogento release nucleic acid.

The present invention also provides kits for carrying out the variousmethods of the present invention.

These and other features and advantages of the present invention aredescribed below in connection with various illustrative embodiments ofthe devices and methods of the present invention.

Definitions

“Nucleic acid” shall have the meaning known in the art and refers to DNA(e.g., genomic DNA, cDNA, or plasmid DNA), RNA (e.g., mRNA, tRNA, orrRNA), and PNA. It can be in a wide variety of forms, including, withoutlimitation, double-stranded or single-stranded configurations, circularform, plasmids, relatively short oligonucleotides, peptide nucleic acidsalso called PNA's (as described in Nielsen et al., Chem. Soc. Rev., 26,73-78 (1997)), and the like. The nucleic acid can be genomic DNA, whichcan include an entire chromosome or a portion of a chromosome. The DNAcan include coding (e.g., for coding mRNA, tRNA, and/or rRNA) and/ornoncoding sequences (e.g., centromeres, telomeres, intergenic regions,introns, transposons, and/or microsatellite sequences). The nucleic acidcan include any of the naturally occurring nucleotides as well asartificial or chemically modified nucleotides, mutated nucleotides, etc.The nucleic acid can include a non-nucleic acid component, e.g.,peptides (as in PNA's), labels (radioactive isotopes or fluorescentmarkers), and the like.

“Nucleic acid-containing material” refers to a source of nucleic acidsuch as a cell (e.g., white blood cell, enucleated red blood cell), anuclei, or a virus, or any other composition that houses a structurethat includes nucleic acid (e.g., plasmid, cosmid, or viroid,archeobacteriae). The cells can be prokaryotic (e.g., gram positive orgram negative bacteria) or eukaryotic (e.g., blood cell or tissue cell).If the nucleic acid-containing material is a virus, it can include anRNA or a DNA genome; it can be virulent, attenuated, or noninfectious;and it can infect prokaryotic or eukaryotic cells. The nucleicacid-containing material can be naturally occurring, artificiallymodified, or artificially created.

“Isolated” refers to nucleic acid (or nucleic acid-containing material)that has been separated from at least a portion of the inhibitors (i.e.,at least a portion of at least one type of inhibitor) in a sample. Thisincludes separating desired nucleic acid from other materials, e.g.,cellular components such as proteins, lipids, salts, and otherinhibitors. More preferably, the isolated nucleic acid is substantiallypurified. “Substantially purified” refers to isolating nucleic acid ofat least 3 picogram per microliter (pg/μL), preferably at least 2nanogram/microliter (ng/μL), and more preferably at least 15 ng/μL,while reducing the inhibitor amount from the original sample by at least20%, preferably by at least 80% and more preferably by at least 99%. Thecontaminants are typically cellular components and nuclear componentssuch as heme and related products (hemin, hematin) and metal ions,proteins, lipids, salts, etc., other than the solvent in the sample.Thus, the term “substantially purified” generally refers to separationof a majority of inhibitors (e.g., heme and it degradation products)from the sample, so that compounds capable of interfering with thesubsequent use of the isolated nucleic acid are at least partiallyremoved.

“Adheres to” or “adherence” or “binding” refer to reversible retentionof inhibitors to an optional solid phase material via a wide variety ofmechanisms, including weak forces such as Van der Waals interactions,electrostatic interactions, affinity binding, or physical trapping. Theuse of this term does not imply a mechanism of action, and includesadsorptive and absorptive mechanisms.

“Solid phase material” (which can optionally be included within a devicein methods of the present invention) refers to an inorganic and/ororganic material, preferably a polymer made of repeating units, whichmay be the same or different, of organic and/or inorganic compounds ofnatural and/or synthetic origin. This includes homopolymers andheteropolymers (e.g., copolymers, terpolymers, tetrapolymers, etc.,which may be random or block, for example). This term includes fibrousor particulate forms of a polymer, which can be readily prepared bymethods well-known in the art. Such materials typically form a porousmatrix, although for certain embodiments, the solid phase also refers toa solid surface, such as a nonporous sheet of polymeric material.

The optional solid phase material may include capture sites. “Capturesites” refer to sites on the solid phase material to which a materialadheres. Typically, the capture sites include functional groups ormolecules that are either covalently attached or otherwise attached(e.g., hydrophobically attached) to the solid phase material.

The phrase “coating reagent coated on the solid phase material” refersto a material coated on at least a portion of the solid phase material,e.g., on at least a portion of the fibril matrix and/or sorptiveparticles.

“Surfactant” refers to a substance that lowers the surface orinterfacial tension of the medium in which it is dissolved.

“Strong base” refers to a base that is completely dissociated in water,e.g., NaOH.

“Polyelectrolyte” refers to an electrolyte that is a charged polymer,typically of relatively high molecular weight, e.g., polystyrenesulfonic acid.

“Selectively permeable polymeric barrier” refers to a polymeric barrierthat allows for selective transport of a fluid based on size and charge.

“Concentrated region” refers to a region of a sample that has a higherconcentration of nucleic acid-containing material, nuclei, and/ornucleic acid, which can be in a pellet form, relative to the lessconcentrated region.

“Substantially separating” as used herein, particularly in the contextof separating a concentrated region of a sample from a less concentratedregion of a sample, means removing at least 40% of the total amount ofnucleic acid (whether it be free, within nuclei, or within other nucleicacid-containing material) in less than 25% of the total volume of thesample. Preferably, at least 75% of the total amount of nucleic acid inless than 10% of the total volume of sample is separated from theremainder of the sample. More preferably, at least 95% of the totalamount of nucleic acid in less than 5% of the total volume of sample isseparated from the remainder of the sample.

“Inhibitors” refer to inhibitors of enzymes used in amplificationreactions, for example. Examples of such inhibitors typically includeiron ions or salts thereof (e.g., Fe²⁺ or salts thereof) and other metalsalts (e.g., alkali metal ions, transition metal ions). Other inhibitorscan include proteins, peptides, lipids, carbohydrates, heme and itsdegradation products, urea, bile acids, humic acids, polysaccharides,cell membranes, and cytosolic components. The major inhibitors in humanblood for PCR are hemoglobin, lactoferrin, and IgG, which are present inerythrocytes, leukocytes, and plasma, respectively. The methods of thepresent invention separate at least a portion of the inhibitors (i.e.,at least a portion of at least one type of inhibitor) from nucleicacid-containing material. As discussed herein, cells containinginhibitors can be the same as the cells containing nuclei or othernucleic acid-containing material. Inhibitors can be contained in cellsor be extracellular. Extracellular inhibitors include all inhibitors notcontained within cells, which includes those inhibitors present in serumor viruses, for example.

“Preferentially adhere at least a portion of the inhibitors to the solidphase material” means that one or more types of inhibitors will adhereto the optional solid phase material to a greater extent than nucleicacid-containing material (e.g., nuclei) and/or nucleic acid, andtypically without adhering a substantial portion of the nucleicacid-containing material and/or nuclei to the solid phase material.

“Microfluidic” (where used herein) refers to a device with one or morefluid passages, chambers, or conduits that have at least one internalcross-sectional dimension, e.g., depth, width, length, diameter, etc.,that is less than 500 μm, and typically between 0.1 μm and 500 μm. Inthe devices used in the present invention, the microscale channels orchambers may preferably have at least one cross-sectional dimensionbetween 0.1 μm and 200 μm, more preferably between 0.1 μm and 100 μm,and often between 1 μm and 20 μm. Typically, a microfluidic deviceincludes a plurality of chambers (process chambers, separation chambers,mixing chambers, waste chambers, diluting reagent chambers,amplification reaction chambers, loading chambers, and the like), eachof the chambers defining a volume for containing a sample; and at leastone distribution channel connecting the plurality of chambers of thearray; wherein at least one of the chambers within the array can includea solid phase material (thereby often being referred to as a separationchamber) and/or at least one of the process chambers within the arraycan include a lysing reagent (thereby often being referred to as amixing chamber), for example.

The terms “comprises” and variations thereof do not have a limitingmeaning where these terms appear in the description and claims.

Also herein, the recitations of numerical ranges by endpoints includeall numbers subsumed within that range (e.g., 1 to 5 includes 1, 1.5, 2,2.75, 3, 3.80, 4, 5, etc.).

The above summary of the present invention is not intended to describeeach disclosed embodiment or every implementation of the presentinvention. The description that follows more particularly exemplifiesillustrative embodiments. In several places throughout the application,guidance is provided through lists of examples, which examples can beused in various combinations. In each instance, the recited list servesonly as a representative group and should not be interpreted as anexclusive list. Furthermore, various embodiments are described in whichthe various elements of each embodiment could be used in otherembodiments, even though not specifically described.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a plan view of one exemplary sample processing deviceaccording to the present invention.

FIG. 2 is an enlarged cross-sectional view of a portion of the sampleprocessing device of FIG. 1, taken along line 2-2 in FIG. 1.

FIGS. 3A-3D depict one exemplary method of moving fluid through aprocess array including a process chamber and a valve chamber.

FIG. 4 is a plan view of an alternative process chamber and multiplevalve chambers in accordance with the present invention.

FIG. 5 is a cross-sectional view of another alternative process chamberand valve chamber construction according to the present invention,including optional detection apparatus facing both major sides of thesample processing device.

FIG. 6 is a representation of a device used in certain methods of thepresent invention.

DETAILED DESCRIPTION OF ILLUSTRATIVE EMBODIMENTS OF THE INVENTION

In the following detailed description of illustrative embodiments of theinvention, reference is made to the accompanying figures of the drawingwhich form a part hereof, and in which are shown, by way ofillustration, specific embodiments in which the invention may bepracticed. It is to be understood that other embodiments may be utilizedand structural changes may be made without departing from the scope ofthe present invention.

The present invention provides a sample processing device that can beused in the processing of liquid sample materials (or sample materialsentrained in a liquid) in multiple process chambers to obtain desiredreactions, e.g., PCR amplification, ligase chain reaction (LCR),self-sustaining sequence replication, enzyme kinetic studies,homogeneous ligand binding assays, and other chemical, biochemical, orother reactions that may, e.g., require precise and/or rapid thermalvariations. More particularly, the present invention provides sampleprocessing devices that include one or more process arrays, each ofwhich may preferably include a loading chamber, at least one processchamber, a valve chamber, and conduits for moving fluids between variouscomponents of the process arrays. The devices of the present inventionmay or may not include microfluidic features.

Although various constructions of illustrative embodiments are describedbelow, sample processing devices of the present invention may be similarto those described in, e.g., U.S. Patent Application Publication Nos.US2002/0064885 (Bedingham et al.); US2002/0048533 (Bedingham et al.);US2002/0047003 (Bedingham et al.), and US2003/138779 (Parthasarathy etal.); as well as U.S. Pat. No. 6,627,159 B1 (Bedingham et al.). Thedocuments identified above all disclose a variety of differentconstructions of sample processing devices that could be used tomanufacture sample processing devices according to the principles of thepresent invention.

One illustrative sample processing device manufactured according to theprinciples of the present invention is illustrated in FIGS. 1 & 2, whereFIG. 1 is a plan view of one sample processing device 10 and FIG. 2 isan enlarged cross-sectional view of a portion of the sample processingdevice 10 (taken along line 2-2 in FIG. 1). The sample processing device10 may preferably be in the shape of a circular disc as illustrated inFIG. 1, although any other shape that can be rotated could be used inplace of a circular disc.

The sample processing device 10 includes at least one, and preferablymultiple process arrays 20. If the sample processing device 10 iscircular as depicted, it may be preferred that each of the depictedprocess arrays 20 extends from proximate a center 12 of the sampleprocessing device 10 towards the periphery of the sample processingdevice 10. The process arrays 20 are depicted as being substantiallyaligned radially with respect to the center 12 of the sample processingdevice 10. Although this arrangement may be preferred, it will beunderstood that any arrangement of process arrays 20 may alternativelybe used. Also, although the illustrated sample processing device 10includes four process arrays 20, the exact number of process arraysprovided in connection with a sample processing device manufacturedaccording to the present invention may be greater than or less thanfour.

Each of the process arrays 20 (in the embodiment depicted in FIG. 1)includes a loading chamber 30 connected to a process chamber 40 along aconduit 32. The process arrays 20 also include a valve chamber 60connected to a second process chamber 70 by a conduit 62. The valvechamber 60 may preferably be located within a valve lip 50 extendinginto the area occupied by the process chamber 40 on the sampleprocessing device 10.

It should be understood that a number of the features associated withone or more of the process arrays 20 may be optional. For example, theloading chambers 30 and associated conduits 32 may be optional wheresample material can be introduced directly into the process chambers 40through a different loading structure. At the same time, additionalfeatures may be provided with one or more of the process arrays 20. Forexample, two or more valve chambers 60 may be associated with one ormore of the process arrays 20. Additional valve chambers may beassociated with additional process chambers or other features.

Any loading structure provided in connection with the process arrays 20may be designed to mate with an external apparatus (e.g., a pipette,hollow syringe, or other fluid delivery apparatus) to receive the samplematerial. The loading structure itself may define a volume (as, e.g.,does loading chamber 30 of FIG. 1) or the loading structure may defineno specific volume, but, instead, be a location at which sample materialis to be introduced. For example, the loading structure may be providedin the form of a port through which a pipette or needle is to beinserted. In one embodiment, the loading structure may be, e.g., adesignated location along a conduit that is adapted to receive apipette, syringe needle, etc. The loading may be performed manually orby an automated system (e.g., robotic, etc.). Further, the sampleprocessing device 10 may be loaded directly from another device (usingan automated system or manually).

FIG. 2 is an enlarged cross-sectional view of the processing device 10taken along line 2-2 in FIG. 1. Although sample processing devices ofthe present invention may be manufactured using any number of suitableconstruction techniques, one illustrative construction can be seen inthe cross-sectional view of FIG. 2. The sample processing device 10includes a base layer 14 attached to a valve layer 16. A cover layer 18is attached to the valve layer 16 over the side of the valve layer 16that faces away from the base layer 14.

The layers of sample processing device 10 may be manufactured of anysuitable material or combination of materials. Examples of some suitablematerials for the base layer 14 and/or valve layer 16 include, but arenot limited to, polymeric material, glass, silicon, quartz, ceramics,etc. For those sample processing devices 10 in which the layers will bein direct contact with the sample materials, it may be preferred thatthe material or materials used for the layers be non-reactive with thesample materials. Examples of some suitable polymeric materials thatcould be used for the substrate in many different bioanalyticalapplications may include, but are not limited to, polycarbonate,polypropylene (e.g., isotactic polypropylene), polyethylene, polyester,etc.

The layers making up sample processing device 10 may be attached to eachother by any suitable technique or combination of techniques. Suitableattachment techniques preferably have sufficient integrity such that theattachment can withstand the forces experienced during processing ofsample materials in the process chambers. Examples of some of thesuitable attachment techniques may include, e.g., adhesive attachment(using pressure sensitive adhesives, curable adhesives, hot meltadhesives, etc.), heat sealing, thermal welding, ultrasonic welding,chemical welding, solvent bonding, coextrusion, extrusion casting, etc.and combinations thereof. Furthermore, the techniques used to attach thedifferent layers may be the same or different. For example, thetechnique or techniques used to attach the base layer 14 and the valvelayer 16 may be the same or different as the technique or techniquesused to attach the cover layer 18 and the valve layer 16.

FIG. 2 depicts a process chamber 40 in its cross-sectional view. Alsoseen in FIG. 2 is the valve lip 50 that, in the depicted embodiment islocated within the area occupied by the process chamber, i.e., theprocess chamber area. The process chamber are may preferably be definedby projecting the process chamber boundaries onto either of the majorsides of the sample processing device 10. In the embodiment depicted inFIG. 2, a first major side 15 of the sample processing device 10 isdefined by the lowermost surface of base layer 14 (i.e., the surfacefacing away from valve layer 16) and a second major side 19 is definedby the uppermost surface of cover layer 18 (i.e., the surface facingaway from the valve layer 16). It should be understood that “upper” and“lower” as used herein are with reference to FIG. 2 only and are not tobe construed as limiting the orientation of the sample processing device10 in use.

The valve lip 50 is depicted as extending into the process chamber areaas defined by the outermost boundaries of process chamber 40. Becausethe valve lip 50 is located within the process chamber area, the valvelip 50 may be described as overhanging a portion of the process chamber40 or being cantilevered over a portion of the process chamber 40.

Preferred process chambers of the present invention may include adetection window that allows the detection of one or morecharacteristics of any sample material in the process chamber 40. It maybe preferred that the detection be achieved using selected light, wherethe term “light” refers to electromagnetic energy, whether visible tothe human eye or not. It may be preferred that the light fall within arange of ultraviolet to infrared electromagnetic energy, and, in someinstances, it may be preferred that light include electromagnetic energyin the spectrum visible to the human eye. Furthermore, the selectedlight may be, e.g., light of one or more particular wavelengths, one ormore ranges of wavelengths, one or more polarization states, orcombinations thereof.

In the embodiment depicted in FIG. 2, the detection window may beprovided in the cover layer 18 or in the base layer 14 (or both).Regardless of which component is used as the detection window, thematerials used preferably transmit significant portions of selectedlight. For the purposes of the present invention, significant portionsmay be, e.g., 50% or more of normal incident selected light, morepreferably 75% or more of normal incident selected light. Examples ofsome suitable materials for the detection window include, but are notlimited to, e.g., polypropylenes, polyesters, polycarbonates,polyethylenes, polypropylene-polyethylene copolymers, cyclo-olefinpolymers (e.g., polydicyclopentadiene), etc.

In some instances, it may be preferred that the base layer 14 and/or thecover layer 18 of the sample processing device 10 be opaque such thatthe sample processing device 10 is opaque between the volume of theprocess chamber volume 14 and at least one side of the sample processingdevice 10. By opaque, it is meant that transmission of the selectedlight as described above is substantially prevented (e.g., 5% or less ofsuch normally incident light is transmitted).

Valve chamber 60 is depicted in FIG. 2 and may preferably be at leastpartially located within the valve lip 50 as seen in FIG. 2. At least aportion of the valve chamber 60 may preferably be located between thesecond major side 19 of the sample processing device 10 and at least aportion of the process chamber 40. The valve chamber 60 is alsopreferably isolated from the process chamber 40 by a valve septum 64separating the valve chamber 64 and the process chamber 40, such that aportion of the volume of the process chamber 40 lies between the valveseptum 64 and the first major side 15 of the sample processing device10. In the depicted embodiment, the cover layer 18 is preferably sealedto the valve lip 50 along surface 52 to isolate the valve chamber 60from the process chamber 50.

The valve septum 64 is preferably formed of material in which openingscan be formed by non-contact methods, e.g., laser ablation, etc. As suchthe material or materials used in the septum 64 may include materialsthat preferentially absorb the energy used to open the septum 64. Forexample, the septum 64 may include materials such as, e.g., carbonblack, UV/IR absorbers. etc.

The energy used to form openings in the valve septum 64 can be directedonto the valve septum 64 either through the cover layer 18 or throughthe base layer 14 (or through both). It may be preferred, however, thatthe energy be directed at the valve septum 64 through the cover layer 18to avoid issues that may be associated with directing the energy throughthe sample material in the process chamber 40 before it reaches thevalve septum 64.

One illustrative method of using a process array 120 will now bedescribed with respect to FIGS. 3A-3D, each of which is a plan view ofthe process array in various stages of one illustrative method accordingto the present invention. The process array 120 depicted in each of thefigures includes a loading chamber 130 connected to a process chamber140 through conduit 132. The process array also includes a valve lip 150and a valve chamber 160 located within a portion of the valve lip 150.The valve lip 150 and the valve chamber 160 define a valve septum 164separating and isolating the valve chamber 160 from the process chamber140 before any openings are formed through the valve septum 164. Thevalve septum 164 boundary is depicted as a broken line in the figuresbecause it may not be visible to the naked eye.

Another feature of the process array 120 is a detection window 142through selected light can be transmitted into and/or out of the processchamber 140. The detection window 142 may be formed through either majorside of the device in which process array 120 is located (or throughboth major sides if so desired). In the depicted embodiment, thedetection window 142 may preferably be defined by that portion of thearea occupied by the process chamber 140 that is not also occupied bythe valve lip 150. In another manner of characterizing the detectionwindow 142, the detection window 142 and the valve lip 150 (and/or valvechamber 160 contained therein) may be described as occupying mutuallyexclusive portions of the area of the process chamber 140.

The process array 120 also includes an output process chamber 170connected to the valve chamber 160 through conduit 162. The outputprocess chamber 170 may include, e.g., one or more reagents 172 locatedtherein. The reagent 172 may be fixed within the process chamber 170 orit may be loose within the process chamber. Although depicted in processchamber 170, one or more reagents may be provided at any suitablelocation or locations within the process array 120, e.g., the loadingchamber 130, conduits 132 & 162, process chamber 140, valve chamber 160,etc.

The use of reagents is optional, i.e., sample processing devices of thepresent invention may or may not include any reagents in the processchambers. In another variation, some of the process chambers indifferent process arrays may include a reagent, while others do not. Inyet another variation, different process chambers may contain differentreagents. Further, the interior of the process chamber structures may becoated or otherwise processed to control the adhesion of reagents.

The process chamber 140 (and its associated process chamber area) maypreferably have a length (measured along, e.g., axis 121 in FIG. 3A)that is greater than the width of the process chamber 140, where theprocess chamber width is measured perpendicular to the process chamberlength. As such, the process chamber 140 may be described as“elongated.” It may be preferred that the axis 121 along which theprocess chamber 140 is elongated be aligned with a radial directionextending from an axis of rotation about which the sample processingdevice containing process array is rotated (if rotation is the drivingforce used to effect fluid transfer).

In other aspects, it may be preferred that the detection window 142 beat least coextensive along the length of the process chamber 140 withthe valve septum 164. Although the depicted detection window 142 is asingle unitary feature, it will be understood that more two or moredetection windows could be provided for each process chamber 140. Forexample, a plurality of independent detection windows could bedistributed along the length of the process chamber 140 (e.g., alongsidethe valve septum 164.

Another manner of characterizing the relative sizes of the variousfeatures may be, e.g., that the valve septum 164 extends along thelength of the process chamber area for 30% or more (or, alternatively,for 50% or more) of a maximum length of the process chamber 140 (alongits elongation axis 121). Such a characterization of the dimensions ofvalve septum 164 may be expressed in actual measurements for many sampleprocessing devices, e.g., the valve septum 164 may be described asextending for a length of 1 millimeter or more along the length of theprocess chamber 140.

The first stage of the depicted method is seen in FIG. 3A, where theloading chamber 130 includes sample material 180 located therein. Forthe purposes of the illustrated method, the sample material 180 is wholeblood. After loading, the blood 180 is preferably transferred to theprocess chamber 140 through conduit 132. The transfer may preferably beeffected by rotating the process array 120 about an axis of rotation111. The rotation may preferably occur, for example, in the plane of thepaper on which FIG. 3A is located, although any rotation about point 111in which process chamber 140 is moved in an arc about a point located onthe opposite side of the loading chamber 130 from the process chamber140 may be acceptable. A further description of a preferred process forprocessing whole blood to remove the nucleic acid is provided below.

The process arrays used in sample processing devices of the presentinvention may preferably be “unvented.” As used in connection with thepresent invention, an “unvented process array” is a process array (i.e.,at least two connected chambers) in which the only openings leading intothe process array are located in the loading structure, e.g., theloading chamber. In other words, to reach the process chamber within anunvented process array, sample materials must be delivered to theloading chamber. Similarly, any air or other fluid located within theprocess array before loading of the sample material must also escapefrom the process array through the loading chamber. In contrast, avented process array would include at least one opening outside of theloading chamber. That opening would allow for the escape of any air orother fluid located within the process array before loading.

Moving sample material through sample processing devices that includeunvented process arrays may be facilitated by alternately acceleratingand decelerating the device during rotation, essentially burping thesample materials through the conduits and process chambers. The rotatingmay be performed using at least two acceleration/deceleration cycles,i.e., an initial acceleration, followed by deceleration, second round ofacceleration, and second round of deceleration. It may further behelpful if the acceleration and/or deceleration are rapid. The rotationmay also preferably only be in one direction, i.e., it may not benecessary to reverse the direction of rotation during the loadingprocess. Such a loading process allows sample materials to displace theair in those portions of the process arrays that are located fartherfrom the center of rotation of the device. The actual acceleration anddeceleration rates may vary based on a variety of factors such astemperature, size of the device, distance of the sample material fromthe axis of rotation, materials used to manufacture the devices,properties of the sample materials (e.g., viscosity), etc.

FIG. 3B depicts the process array after movement of the blood 180 intothe process chamber 140. The blood 180 remains in the process chamber140, i.e., does not travel into the valve chamber 160, because the valvechamber 160 is isolated from the process chamber 140 by the valve septum164.

Additional rotation of the process array 120 may preferably result inseparation of the components of the blood 180 into, as seen in FIG. 3C,red blood cells 182, a buffy coat layer 184, and plasma 186. Theseparation is typically a result of centrifugal forces and the relativedensities of the materials.

If the precise volume of the different components in each sample ofblood 180 (or if the volume of the blood sample 180 itself) is notknown, the location of the boundaries between the different separatedlayers may not be known. In connection with the present invention,however, it may preferably be possible to detect the locations of theboundaries between the different separated components.

Such detection may preferably occur through the detection window usingany suitable selected light. The light may be transmitted through orreflected from the blood components 182, 184 & 186 to obtain an image ofthe sample material in the process chamber 140. In another alternative,absorbance of light may be used to detect the boundaries or locations ofone or more selected components. For example, after spinning blood, itmay be possible to detect the interfaces between the packed red bloodcell layer, the buffy layer (white blood cells), and plasma. Afterspinning beads, it may be possible to detect the interface between thepacked bead layer and a supernatant layer.

It may be preferable to determine the location of all features orcharacteristics of the sample material, i.e., the location of allboundaries, including the free surface 187 of the plasma 186. In otherinstances, it may be sufficient to determine the location of only onefeature, e.g., the boundary between the buffy coat layer 184 and theplasma 186, where the detected characteristic provides sufficientinformation to perform the next step in the method.

After the suitable characteristic or characteristics of the materials inthe process chamber 140 have been detected, an opening 168 is preferablyformed in the valve septum 164 at the desired location. In the depictedmethod, the desired location for opening 168 is chosen to remove aportion of the plasma 186 from the process chamber 140. It may bedesirable that substantially all of the plasma 186 be removed, leavingonly a small amount (see 186 r in FIG. 3D) in the process chamber 140.It may be necessary to leave a small amount of plasma in the processchamber 140 to limit or prevent the transfer of red blood cells 182 outof the process chamber 140.

The opening 168 can be formed by any suitable non-contact technique. Onesuch technique may be, e.g., laser ablation of the valve septum 168.Other techniques may include, but are not limited to, e.g., focusedoptical heating, etc.

After the opening 168 is formed, additional rotation of the processarray 120 preferably moves the plasma 186 from the process chamber 140into the valve chamber 160 through opening 168, followed by transferinto the output process chamber 170 through conduit 162. As a result,the plasma 186 is located in the process chamber 170, with a smallremainder of plasma 186 r in the process chamber 140 along with thebuffy coat layer 184 and red blood cells 182.

A portion of another embodiment of a process array 220 including aprocess chamber 240 and valve structures according to the presentinvention is depicted in FIG. 4. In the depicted embodiment, the processchamber 240 is elongated along axis 221 and the process array 220 isdesigned for rotation to provide the force to move fluids. The rotationmay be about point 211 which, in the depicted embodiment, lies on axis221. It should, however, be understood that the point about which theprocess array is rotated is not required to lie on axis 221.

The process chamber 240 is shown in broken lines where the valve lips250 a, 250 b and 250 c extend into the process chamber area and in solidlines where the valve lips 250 a, 250 b and 250 c do not extend into theprocess chamber area. It may be preferred that in those portions of theprocess chamber area that are not occupied by the valve lips 250 a, 250b and 250 c, the process chamber 240 include a detection window 242 thatallows for the transmission of selected light into and/or out of theprocess chamber 240 to allow for detection of sample material 280 in theprocess chamber 240.

The process array 220 also includes valve chambers 260 a, 260 b, and 260c isolated and separated from the process chamber 240. The valvechambers 260 a, 260 b, and 260 c are each in communication with achamber 270 a, 270 b, and 270 c (respectively). The valve chambers 260a, 260 b, and 260 c may be connected to their respective chambers 270 a,27 ob, and 270 c by a conduit as shown in FIG. 4.

Each of the valve chambers 260 a, 260 b, and 260 c may preferably belocated, at least in part, on a valve lip 250 a, 250 b and 250 c(respectively). Each of the valve chambers 260 a, 260 b, and 260c mayalso preferably be isolated and separated from the process chamber 240by a valve septum 264 a, 264 b, and 264 c located within each of thevalve chambers 260 a, 260 b, and 260 c. Each of the valve septums 264 a,264 b, and 264 c is defined, in part, by the broken lines of processchamber 240.

The multiple valve chambers 260 a, 260 b, and 260 c provided inconnection with the process chamber 240 may provide the ability toselectively remove different portions of any sample material in theprocess chamber and to move that sample material to different chambers270 a, 270 b, and 270 c. For example, a first portion of sample material280 in the process chamber 240 may be moved into chamber 270 a byforming an opening 268 a in valve septum 264 a of valve chamber 260 a.

After moving the first portion of sample material 280 into chamber 270 athrough opening 268 a in valve chamber 260 a, another opening 268 b maybe provided in valve septum 264 b of valve chamber 260 b to move asecond portion of the sample material 280 into chamber 270 b. The secondportion will typically include the sample material 280 located betweenopenings 268 a and 268 b. The distance separating those two openingsalong the length of the process chamber 240 is indicated by x in FIG. 4.As a result, the volume of the second portion of sample material 280 canbe determined if the cross-sectional area of the process chamber 240(taken in a plane perpendicular to the axis 221) is known. As a result,it may be possible to move a known or selected volume of sample materialinto chamber 270 b by forming openings 268 a and 268 b a selecteddistance apart from each other.

The process chamber 240 also includes a third valve chamber 260 clocated in a valve lip 250 c at the end of the process chamber 240farthest from the point 211 about which the process array 220 may berotated. The valve lip 250 c extends over the entire width of theprocess chamber 240 (in contrast to the valve lips 250 a and 250 b thatextend over only a portion of the width of the process chamber 240).

FIG. 5 depicts another process chamber 340 in connection with thepresent invention in cross-section. The process chamber 340 is formed ina sample processing device 310 that includes a base layer 313,intermediate layer 314, valve layer 316 and cover layer 318. The variouslayers may be attached to each other by any suitable combination oftechniques.

Although the layers are depicted as single, homogeneous constructions,it will be understood that one or more of the layers could be formed ofmultiple materials and/or layers. Furthermore, it may be possible tocombine some of the layers. For example, layers 313 and 314 may becombined (as an example, see layer 14 in the cross-sectional view ofFIG. 2). Alternatively, it may be possible to combine layers 314 and 316into a single structure that could be formed by, e.g., molding,extrusion, etc.

The construction seen in FIG. 5 includes a valve chamber 360 separatedfrom the process chamber 340 by a valve septum 364. The valve chamber360 is further defined by the cover layer 318. A device 390 is alsodepicted in FIG. 5 that can be used to, e.g., form an opening in thevalve septum 364. The device 390 may be, e.g., a laser, etc. that canpreferably deliver the energy necessary to form an opening in the valveseptum 364 without forming an opening in the cover layer 318.

If the energy required to form openings in the valve septum 364 can bedirected through the cover layer 318, then the base layer 313 may beformed of any material that may block such energy. For example, the baselayer 313 may be made of, e.g., a metallic foil or other material. Ifthe valve layer 316 and/or valve septum 364 allow for the passage ofsufficient amounts of selected wavelengths of light, it may be possibleto detect sample material in the process chamber 340 through the valvelayer 316 and/or valve septum 364.

If, alternatively, the valve layer 316 and valve septum 364 block thepassage of light such that detection of sample material in the processchamber 340 cannot be performed, then it may be desirable to detectsample material in the process chamber 340 through the base layer 313.Such detection may be accomplished using detection device 392 as seen inFIG. 5 that can detect sample material in the process chamber 340through the layer 313. In some instances, it may be possible to formopenings in the valve septum 364 using device 392 directing energythrough layer 313 (if the passage of such energy through sample materialin the process chamber 340 is acceptable).

Illustrative Method using Whole Blood

The present invention also provides methods and kits for isolatingnucleic acid from a whole blood that includes nucleic acid (e.g., DNA,RNA, PNA), which is included within nuclei-containing cells (e.g., whiteblood cells).

It should be understood that although the methods are directed toisolating nucleic acid from a sample, the methods do not necessarilyremove the nucleic acid from the nucleic acid-containing material (e.g.,nuclei). That is, further steps may be required to further separate thenucleic acid from the nuclei, for example.

Certain methods of the present invention may involve ultimatelyseparating nucleic acid from inhibitors, such as heme and degradationproducts thereof (e.g., iron salts), which are undesirable because theycan inhibit amplification reactions (e.g., as are used in PCRreactions). More specifically, certain methods of the present inventionmay involve separating at least a portion of the nucleic acid in asample from at least a portion of at least one type of inhibitor.Preferred methods may involve removing substantially all the inhibitorsin a sample containing nucleic acid such that the nucleic acid issubstantially pure. For example, the final concentration ofiron-containing inhibitors may preferably be no greater than about 0.8micromolar (μM), which is the current level tolerated in conventionalPCR systems.

In order to get clean DNA from whole blood, removal of hemoglobin aswell as plasma proteins is typically desired. When red blood cells arelysed, heme and related compounds are released that inhibit TaqPolymerase. The normal hemoglobin concentration in whole blood is 15grams (g) per 100 milliliters (mL) based on which the concentration ofheme in hemolysed whole blood is around 10 millimolar (mM). For PCR towork out satisfactorily, the concentration of heme should be reduced tothe micromolar (μM) level. This can be achieved, for example, bydilution or by removal of inhibitors using a material that bindsinhibitors.

In one embodiment, the present invention provides a method of isolatingnucleic acid from whole blood, the method includes: providing a devicethat includes a loading chamber and a variable valved process chamber;placing whole blood in the loading chamber; transferring the whole bloodto a valved process chamber; centrifuging the whole blood in the valvedprocess chamber to form a plasma layer (often the upper layer), a redblood cell layer (often the lower layer), and an interfacial layer(located between the plasma layer and the red blood cell layer) thatincludes white blood cells; removing at least a portion of theinterfacial layer; and lysing the white blood cells in the separatedinterfacial layer and optionally lysing the nuclei therein to releaseinhibitors and/or nucleic acid. In certain embodiments, the lysinginvolves subjecting the white blood cells to a strong base with optionalheating to release nucleic acid. If desired, the method can furtherinclude adjusting the pH of the sample that includes the releasednucleic acid to be within a range of 7.5 to 9. Alternatively, the lysingcan involve subjecting the white blood cells to a surfactant.

If desired, before, simultaneously with, or after lysing the white bloodcells, the method can include transferring the separated interfaciallayer to a separation chamber for contact with solid phase material topreferentially adhere at least a portion of the inhibitors to the solidphase material. More specifically, in certain embodiments of thismethod, the device further includes a separation chamber having a solidphase material therein. The solid phase material preferably includescapture sites (e.g., chelating functional groups), a coating reagentcoated on the solid phase material, or both; wherein the coating reagentis selected from the group consisting of a surfactant, a strong base, apolyelectrolyte, a selectively permeable polymeric barrier, andcombinations thereof.

When a solid phase material is present, the method includes contactingthe lysed sample with the solid phase material in the separation chamberto preferentially adhere at least a portion of the inhibitors to thesolid phase material; wherein lysing can occur before, simultaneouswith, or after contacting the solid phase material. The method typicallythen includes separating at least a portion of the nuclei and/or nucleicacid from the solid phase material having at least a portion of theinhibitors adhered thereto.

In certain embodiments wherein no solid phase material is used, thismethod can involve diluting the lysed sample with water (preferably,RNAse-free sterile water) or buffer to reduce the inhibitorconcentration to that which would not interfere with an amplificationmethod; optionally further lysing the nuclei to release nucleic acid;optionally heating the sample to denature proteins and optionallyadjusting the pH of the sample that includes released nucleic acid andoptionally carrying out PCR. Diluting can be accomplished withsufficient water to reduce the concentration of heme to less than 2micromolar. Alternatively, diluting can be accomplished with sufficientwater to form a 2× to 1000× dilution of the lysed sample.

Alternatively, if desired, prior to lysing the white blood cells, themethod can include diluting the separated interfacial layer of thesample with water or buffer, optionally further concentrating thediluted layer to increase the concentration of nucleic acid material,optionally separating the further concentrated region, and optionallyrepeating this process of dilution followed by concentration andseparation to reduce the inhibitor concentration to that which would notinterfere with an amplification method.

Referring to FIG. 6, an example of one potentially preferred embodimentof the device suitable for use with these embodiments includes a loadingchamber 670, a variable valved process chamber 672, an optionalseparation chamber 676, an eluting reagent chamber 678, a waste chamber680, and an optional amplification chamber 682. These chambers are influid communication with each other such that a whole blood sample canbe loaded into the loading chamber 670, which can then be transferred tothe variable valved process chamber 672. Upon centrifuging the wholeblood in the valved process chamber 672 to form a plasma layer (oftenthe upper layer), a red blood cell layer (often the lower layer), and aninterfacial layer that includes white blood cells, at least a portion(and preferably a substantial portion) of the interfacial layer istransferred to the optional separation chamber 676 to separate the whiteblood cells (buffy coat) from at least the red blood cell layer andpreferably from both of the other two (the plasma layer and the redblood cell layer) layers of the whole blood, which can be transferred tothe optional waste chamber 680. Therein the white blood cells in thebuffy coat can be lysed to release inhibitors and nuclei and/or nucleicacid. If the separation chamber 676 includes a solid phase material, theprocess can include preferentially adhering at least a portion of theinhibitors to the solid phase material. The eluting reagent in theeluting reagent chamber 678 is then transferred to the separationchamber 676 to remove at least a portion of the target nucleicacid-containing material and/or nucleic acid. In certain embodiments,this material can be directly transferred to an amplification reactionchamber 682 for carrying out a PCR process, for example. Theamplification reaction chamber 682 can optionally include pre-depositedreactants for the amplification reaction (e.g., PCR).

Lysing Reagents and Conditions

For certain embodiments of the invention, at some point during theprocess, cells within the sample, particularly nucleic acid-containingcells (e.g., white blood cells, bacterial cells, viral cells) are lysedto release the contents of the cells and form a sample (i.e., a lysate).Lysis, as used herein, is the physical disruption of the membranes ofthe cells, referring to the outer cell membrane and, when present, thenuclear membrane. This can be done using standard techniques, such as byhydrolyzing with proteinases followed by heat inactivation ofproteinases, treating with surfactants (e.g., nonionic surfactants orsodium dodecyl sulfate), guanidinium salts, or strong bases (e.g.,NaOH), disrupting physically (e.g., with ultrasonic waves), boiling, orheating/cooling (e.g., heating to at least 55° C. (typically to 95° C.)and cooling to room temperature or below (typically to 8° C.)), whichcan include a freezing/thawing process. Typically, if a lysing reagentis used, it is in aqueous media, although organic solvents can be used,if desired.

Lysing of red blood cells (RBC's) without the destruction of white bloodcells (WBC's) in whole blood can occur to release inhibitors through theuse of water (i.e., aqueous dilution) as the lysing agent (i.e., lysingreagent). Alternatively, ammonium chloride or quaternary ammonium saltscan also be used to break RBC's. The RBC's can also be lysed byhypotonic shock with the use of a hypotonic buffer. The intact WBC's ortheir nuclei can be recovered by centrifugation, for example.

Typically, a stronger lysing reagent, such as a surfactant, can be usedto lyse RBC's as well as nucleic acid-containing cells (e.g., whiteblood cells (WBC's), bacterial cells, viral cells) to releaseinhibitors, nuclei, and/or nucleic acid. For example, a nonionicsurfactant can be used to lyse RBC's as well as WBC's while leaving thenuclei intact. Nonionic surfactants, cationic surfactants, anionicsurfactants, and zwitterionic surfactants can be used to lyse cells.Particularly useful are nonionic surfactants. Combinations ofsurfactants can be used if desired. A nonionic surfactant such as TRITONX-100 can be added to a TRIS buffer containing sucrose and magnesiumsalts for isolation of nuclei.

The amount of surfactant used for lysing is sufficiently high toeffectively lyse the sample, yet sufficiently low to avoidprecipitation, for example. The concentration of surfactant used inlysing procedures is typically at least 0.1 wt-%, based on the totalweight of the sample. The concentration of surfactant used in lysingprocedures is typically no greater than 4.0 wt-%, and preferably, nogreater than 1.0 wt-%, based on the total weight of the sample. Theconcentration is usually optimized in order to obtain complete lysis inthe shortest possible time with the resulting mixture being PCRcompatible. In fact, the nucleic acid in the formulation added to thePCR cocktail should allow for no inhibition of real-time PCR.

If desired, a buffer can be used in admixture with the surfactant.Typically, such buffers provide the sample with a pH of at least 7, andtypically no more than 9.

Typically, an even stronger lysing reagent, such as a strong base, canbe used to lyse any nuclei contained in the nucleic acid-containingcells (as in white blood cells) to release nucleic acid. For example,the method described in U.S. Pat. No. 5,620,852 (Lin et al.), whichinvolves extraction of DNA from whole blood with alkaline treatment(e.g., NaOH) at room temperature in a time frame as short as 1 minute,can be adapted to certain methods of the present invention. Generally, awide variety of strong bases can be used to create an effective pH(e.g., 8-13, preferably 13) in an alkaline lysis procedure. The strongbase is typically a hydroxide such as NaOH, LiOH, KOH; hydroxides withquaternary nitrogen-containing cations (e.g., quaternary ammonium) aswell as bases such as tertiary, secondary or primary amines. Typically,the concentration of the strong base is at least 0.01 Normal (N), andtypically, no more than 1 N. Typically, the mixture can then beneutralized, particularly if the nucleic acid is to subjected to PCR. Inanother procedure, heating can be used subsequent to lysing with base tofurther denature proteins followed by neutralizing the sample.

One can also use Proteinase K with heat followed by heat inactivation ofproteinase K at higher temperatures for isolation of nucleic acids fromthe nuclei or WBC.

One can also use a commercially available lysing agent andneutralization agent such as in Sigma's Extract-N-Amp Blood PCR kitscaled down to, e.g., microfluidic dimensions if desired. Stonger lysingsolutions such as POWERLYSE from GenPoint (Oslo, Norway) for lysingdifficult bacteria such as Staphylococcus, Streptococcus, etc. can beused to advantage in certain methods of the present invention.

In another procedure, a boiling method can be used to lyse cells andnuclei, release DNA, and precipitate hemoglobin simultaneously. The DNAin the supernatant can be used directly for PCR without a concentrationstep, making this procedure useful for low copy number samples.

For infectious diseases, it may be necessary to analyze bacterial orviruses from whole blood. For example, in the case of bacteria, whiteblood cells may be present in conjunction with bacterial cells. In adevice, it would be possible to lyse red blood cells to releaseinhibitors, and then separate out bacterial cells and white blood cellsby centrifugation, for example, prior to further lysing. Thisconcentrated slug of nucleic acid-containing cells (bacterial and whiteblood cells/nuclei) can be moved further into a chamber for removal ofinhibitors. Then, the bacterial cells, for example, can be lysed.

Bacterial cell lysis, depending on the type, may be accomplished usingheat. Alternatively, bacterial cell lysis can occur using enzymaticmethods (e.g., lysozyme, mutanolysin) or chemical methods. The bacterialcells are preferably lysed by alkaline lysis.

The use of bacteria for propagation of plasmids is common in the studyof genomics, analytic molecular biology, preparatory molecular biology,etc. In the case of the bacterium containing plasmid, genetic materialfrom both the bacterium and the plasmid are present. A clean-upprocedure to separate cellular proteins and cellular fragments fromgenomic DNA can be carried out using a method of the present invention.The supernatant thus obtained, which contains the plasmid DNA, is calledthe “cleared lysate.” The cleared lysate can be further purified using avariety of means, such as anion-exchange chromatography, gel filtration,or precipitation with alcohol.

In a specific example of a protocol for bacterial cultures, which can beincorporated into a device, an E. Coli cell culture is centrifuged andresuspended in TE buffer (10 mM TRIS, 1 mM EDTA, pH 7.5) and lysed bythe addition of 0.1 M NaOH/1% SDS (sodium dodecyl sulfate). The celllysis is stopped by the addition of 1 volume of 3 M (three molar)potassium acetate (pH 4.8) and the supernatant centrifuged. The celllysate is further purified to get clean plasmid DNA.

Plasma and serum represent the majority of specimens submitted formolecular testing that include viruses. After fractionation of wholeblood, plasma or serum samples can be used for the extraction of viruses(i.e., viral particles). For example, to isolate DNA from viruses, itmay be possible to first separate out the serum by spinning blood. Bythe use of the variable valve, the serum alone can be emptied intoanother chamber. The serum can then be centrifuged to concentrate thevirus or can be used directly in subsequent lysis steps after removal ofthe inhibitors using a solid phase material, for example, as describedherein. The solid phase material could absorb the solution such that thevirus particles do not go through the material. The virus particles canthen be eluted out in a small elution volume. The virus can be lysed byheat or by enzymatic or chemical means, for example, by the use ofsurfactants, and used for downstream applications, such as PCR orreal-time PCR. In cases where viral RNA is required, it may be necessaryto have an RNAse inhibitor added to the solution to prevent degradationof RNA.

Optional Solid Phase Material

For certain embodiments of the invention, it has been found thatinhibitors will adhere to solid phase materials that include a solidmatrix in any form (e.g., particles, fibrils, a membrane), preferablywith capture sites (e.g., chelating functional groups) attached thereto,a coating reagent (preferably, surfactant) coated on the solid phasematerial, or both. The coating reagent can be a cationic, anionic,nonionic, or zwitterionic surfactant. Alternatively, the coating reagentcan be a polyelectrolyte or a strong base. Various combinations ofcoating reagents can be used if desired.

The solid phase material useful in the methods of the present inventionmay include a wide variety of organic and/or inorganic materials thatretain inhibitors such as heme and heme degradation products,particularly iron ions, for example. Such materials are functionalizedwith capture sites (preferably, chelating groups), coated with one ormore coating reagents (e.g., surfactants, polyelectrolytes, or strongbases), or both. Typically, the solid phase material includes an organicpolymeric matrix.

Generally suitable materials are chemically inert, physically andchemically stable, and compatible with a variety of biological samples.Examples of solid phase materials include silica, zirconia, aluminabeads, metal colloids such as gold, gold-coated sheets that have beenfunctionalized through mercapto chemistry, for example, to generatecapture sites. Examples of suitable polymers include for example,polyolefins and fluorinated polymers. The solid phase material istypically washed to remove salts and other contaminants prior to use. Itcan either be stored dry or in aqueous suspension ready for use. Thesolid phase material is preferably used in a flow-through receptacle,for example, such as a pipet, syringe, or larger column, microtiterplate, or other device, although suspension methods that do not involvesuch receptacles could also be used.

The solid phase material useful in the methods of the present inventioncan include a wide variety of materials in a wide variety of forms. Forexample, it can be in the form of particles or beads, which may be looseor immobilized, fibers, foams, frits, microporous film, membrane, or asubstrate with microreplicated surface(s). If the solid phase materialincludes particles, they are preferably uniform, spherical, and rigid toensure good fluid flow characteristics.

For flow-through applications of the present invention, such materialsare typically in the form of a loose, porous network to allow uniformand unimpaired entry and exit of large molecules and to provide a largesurface area. Preferably, for such applications, the solid phasematerial has a relatively high surface area, such as, for example, morethan one meter squared per gram (m²/g). For applications that do notinvolve the use of a flow-through device, the solid phase material mayor may not be in a porous matrix. Thus, membranes can also be useful incertain methods of the present invention.

For applications that use particles or beads, they may be introduced tothe sample or the sample introduced into a bed of particles/beads andremoved therefrom by centrifuging, for example. Alternatively,particles/beads can be coated (e.g., pattern coated) onto an inertsubstrate (e.g., polycarbonate or polyethylene), optionally coated withan adhesive, by a variety of methods (e.g., spray drying). If desired,the substrate can be microreplicated for increased surface area andenhanced clean-up. It can also be pretreated with oxygen plasma, e-beamor ultraviolet radiation, heat, or a corona treatment process. Thissubstrate can be used, for example, as a cover film, or laminated to acover film, on a reservoir in a device.

In one embodiment, the solid phase material includes a fibril matrix,which may or may not have particles enmeshed therein. The fibril matrixcan include any of a wide variety of fibers. Typically, the fibers areinsoluble in an aqueous environment. Examples include glass fibers,polyolefin fibers, particularly polypropylene and polyethylenemicrofibers, aramid fibers, a fluorinated polymer, particularly,polytetrafluoroethylene fibers, and natural cellulosic fibers. Mixturesof fibers can be used, which may be active or inactive toward binding ofnucleic acid. Preferably, the fibril matrix forms a web that is at leastabout 15 microns, and no greater than about 1 millimeter, and morepreferably, no greater than about 500 microns thick.

If used, the particles are typically insoluble in an aqueousenvironment. They can be made of one material or a combination ofmaterials, such as in a coated particle. They can be swellable ornonswellable, although they are preferably nonswellable in water andorganic liquids. Preferably, if the particle is doing the adhering, itis made of nonswelling, hydrophobic material. They can be chosen fortheir affinity for the nucleic acid. Examples of some water swellableparticles are described in U.S. Pat. Nos. 4,565,663 (Errede et al.),4,460,642 (Errede et al.), and 4,373,519 (Errede et al.). Particles thatare nonswellable in water are described in U.S. Pat. Nos. 4,810,381(Hagen et al.), 4,906,378 (Hagen et al.), 4,971,736 (Hagen et al.); and5,279,742 (Markell et al.). Preferred particles are polyolefinparticles, such as polypropylene particles (e.g., powder). Mixtures ofparticles can be used, which may be active or inactive toward binding ofnucleic acid.

If coated particles are used, the coating is preferably an aqueous- ororganic-insoluble, nonswellable material. The coating may or may not beone to which nucleic acid will adhere. Thus, the base particle that iscoated can be inorganic or organic. The base particles can includeinorganic oxides such as silica, alumina, titania, zirconia, etc., towhich are covalently bonded organic groups. For example, covalentlybonded organic groups such as aliphatic groups of varying chain length(C2, C4, C8, or C18 groups) can be used.

Examples of suitable solid phase materials that include a fibril matrixare described in U.S. Pat. Nos. 5,279,742 (Markell et al.), 4,906,378(Hagen et al.), 4,153,661 (Ree et al.), 5,071,610 (Hagen et al.),5,147,539 (Hagen et al.), 5,207,915 (Hagen et al.), and 5,238,621 (Hagenet al.). Such materials are commercially available from 3M Company (St.Paul, Minn.) under the trade designations SDB-RPS (Styrene-DivinylBenzene Reverse Phase Sulfonate, 3M Part No. 2241), cation-SR membrane(3M Part No. 2251), C-8 membrane (3M Part No. 2214), and anion-SRmembrane (3M Part No. 2252).

Those that include a polytetrafluoroethylene matrix (PTFE) areparticularly preferred. For example, U.S. Pat. No. 4,810,381 (Hagen etal.) discloses a solid phase material that includes: apolytetrafluoroethylene fibril matrix, and nonswellable sorptiveparticles enmeshed in the matrix, wherein the ratio of nonswellablesorptive particles to polytetrafluoroethylene being in the range of 19:1to 4:1 by weight, and further wherein the composite solid phase materialhas a net surface energy in the range of 20 to 300 milliNewtons permeter. U.S. Pat. No. RE 36,811 (Markell et al.) discloses a solid phaseextraction medium that includes: a PTFE fibril matrix, and sorptiveparticles enmeshed in the matrix, wherein the particles include morethan 30 and up to 100 weight percent of porous organic particles, andless than 70 to 0 weight percent of porous (organic-coated or uncoated)inorganic particles, the ratio of sorptive particles to PTFE being inthe range of 40:1 to 1:4 by weight.

Particularly preferred solid phase materials are available under thetrade designation EMPORE from the 3M Company, St. Paul, Minn. Thefundamental basis of the EMPORE technology is the ability to create aparticle-loaded membrane, or disk, using any sorbent particle. Theparticles are tightly held together within an inert matrix ofpolytetrafluoroethylene (90% sorbent: 10% PTFE, by weight). The PTFEfibrils do not interfere with the activity of the particles in any way.The EMPORE membrane fabrication process results in a denser, moreuniform extraction medium than can be achieved in a traditional SolidPhase Extraction (SPE) column or cartridge prepared with the same sizeparticles.

In another preferred embodiment, the solid phase (e.g., a microporousthermoplastic polymeric support) has a microporous structurecharacterized by a multiplicity of spaced, randomly dispersed,nonuniform shaped, equiaxed particles of thermoplastic polymer connectedby fibrils. Particles are spaced from one another to provide a networkof micropores therebetween. Particles are connected to each other byfibrils, which radiate from each particle to the adjacent particles.Either, or both, the particles or fibrils may be hydrophobic. Examplesof preferred such materials have a high surface area, often as high as40 meters²/gram as measured by Hg surface area techniques and pore sizesup to about 5 microns.

This type of fibrous material can be made by a preferred technique thatinvolves the use of induced phase separation. This involves meltblending a thermoplastic polymer with an immiscible liquid at atemperature sufficient to form a homogeneous mixture, forming an articlefrom the solution into the desired shape, cooling the shaped article soas to induce phase separation of the liquid and the polymer, and toultimately solidify the polymer and remove a substantial portion of theliquid leaving a microporous polymer matrix. This method and thepreferred materials are described in detail in U.S. Pat. Nos. 4,726,989(Mrozinski), 4,957,943 (McAllister et al.), and 4,539,256 (Shipman).Such materials are referred to as thermally induced phase separationmembranes (TIPS membranes) and are particularly preferred.

Other suitable solid phase materials include nonwoven materials asdisclosed in U.S. Pat. No. 5,328,758 (Markell et al.). This materialincludes a compressed or fused particulate-containing nonwoven web(preferably blown microfibrous) that includes high sorptive-efficiencychromatographic grade particles.

Other suitable solid phase materials include those known as HIPE Foams,which are described, for example, in U.S. Pat. Publication No.2003/0011092 (Tan et al.). “HIPE” or “high internal phase emulsion”means an emulsion that includes a continuous reactive phase, typicallyan oil phase, and a discontinuous or co-continuous phase immiscible withthe oil phase, typically a water phase, wherein the immiscible phaseincludes at least 74 volume percent of the emulsion. Many polymericfoams made from HIPE's are typically relatively open-celled. This meansthat most or all of the cells are in unobstructed communication withadjoining cells. The cells in such substantially open-celled foamstructures have intercellular windows that are typically large enough topermit fluid transfer from one cell to another within the foamstructure.

The solid phase material can include capture sites for inhibitors.Herein, “capture sites” refer to groups that are either covalentlyattached (e.g., functional groups) or molecules that are noncovalently(e.g., hydrophobically) attached to the solid phase material.

Preferably, the solid phase material includes functional groups thatcapture the inhibitors. For example, the solid phase material mayinclude chelating groups. In this context, “chelating groups” are thosethat are polydentate and capable of forming a chelation complex with ametal atom or ion (although the inhibitors may or may not be retained onthe solid phase material through a chelation mechanism). Theincorporation of chelating groups can be accomplished through a varietyof techniques. For example, a nonwoven material can hold beadsfunctionalized with chelating groups. Alternatively, the fibers of thenonwoven material can be directly functionalized with chelating groups.

Examples of chelating groups include, for example, —(CH₂—C(O)OH)₂,tris(2-aminoethyl)amine groups, iminodiacetic acid groups,nitrilotriacetic acid groups. The chelating groups can be incorporatedinto a solid phase material through a variety of techniques. They can beincorporated in by chemically synthesizing the material. Alternatively,a polymer containing the desired chelating groups can be coated (e.g.,pattern coated) on an inert substrate (e.g., polycarbonate orpolyethylene). If desired, the substrate can be microreplicated forincreased surface area and enhanced clean-up. It can also be pretreatedwith oxygen plasma, e-beam or ultraviolet radiation, heat, or a coronatreatment process. This substrate can be used, for example, as a coverfilm, or laminated to a cover film, on a reservoir in a device.

Chelating solid phase materials are commercially available and could beused as the solid phase material in the present invention. For example,for certain embodiments of the present invention, EMPORE membranes thatinclude chelating groups such as iminodiacetic acid (in the form of thesodium salt) are preferred. Examples of such membranes are disclosed inU.S. Pat. No. 5,147,539 (Hagen et al.) and commercially available asEMPORE Extraction Disks (47 mm, No. 2271 or 90 mm, No. 2371) from the 3MCompany. For certain embodiments of the present invention,ammonium-derivatized EMPORE membranes that include chelating groups arepreferred. To put the disk in the ammonium form, it can be washed with50 mL of 0.1M ammonium acetate buffer at pH 5.3 followed with severalreagent water washes.

Examples of other chelating materials include, but are not limited to,crosslinked polystyrene beads available under the trade designationCHELEX from Bio-Rad Laboratories, Inc. (Hercules, Calif.), crosslinkedagarose beads with tris(2-aminoethyl)amine, iminodiacetic acid,nitrilotriacetic acid, polyamines and polyimines as well as thechelating ion exchange resins commercially available under the tradedesignation DUOLITE C-467 and DUOLITE GT73 from Rohm and Haas(Philadelphia, Pa.), AMBERLITE IRC-748, DIAION CR11, DUOLITE C647.

Typically, a desired concentration density of chelating groups on thesolid phase material is about 0.02 nanomole per millimeter squared,although it is believed that a wider range of concentration densities ispossible.

Other types of capture materials include anion exchange materials,cation exchange materials, activated carbon, reverse phase, normalphase, styrene-divinyl benzene, alumina, silica, zirconia, and metalcolloids. Examples of suitable anion exchange materials include stronganion exchangers such as quaternary ammonium, dimethylethanolamine,quaternary alkylamine, trimethylbenzyl ammonium, anddimethylethanolbenzyl ammonium usually in the chloride form, and weakanion exchangers such as polyamine. Examples of suitable cation exchangematerials include strong cation exchangers such as sulfonic acidtypically in the sodium form, and weak cation exchangers such ascarboxylic acid typically in the hydrogen form. Examples of suitablecarbon-based materials include EMPORE carbon materials, carbon beads,Examples of suitable reverse phase C8 and C18 materials include silicabeads that are end-capped with octadecyl groups or octyl groups andEMPORE materials that have C8 and C18 silica beads (EMPORE materials areavailable from 3M Co., St. Paul, Minn.). Examples of normal phasematerials include hydroxy groups and dihydroxy groups.

Commercially available materials can also be modified or directly usedin methods of the present invention. For example, solid phase materialsavailable under the trade designation LYSE AND GO (Pierce, Rockford,Ill.), RELEASE-IT (CPG, NJ), GENE FIZZ (Eurobio, France), GENE RELEASER(Bioventures Inc., Murfreesboro, Tenn.), and BUGS N BEADS (GenPoint,Oslo, Norway), as well as Zymo's beads (Zymo Research, Orange, Calif.)and Dynal's beads (Dynal, Oslo, Norway) can be incorporated into themethods of the present invention, particularly into a device as thesolid phase capture material.

In certain embodiments of such methods, the solid phase materialincludes a coating reagent. The coating reagent is preferably selectedfrom the group consisting of a surfactant, a strong base, apolyelectrolyte, a selectively permeable polymeric barrier, andcombinations thereof. In certain embodiments of such methods, the solidphase material includes a polytetrafluoroethylene fibril matrix,sorptive particles enmeshed in the matrix, and a coating reagent coatedon the solid phase material, wherein the coating reagent is selectedfrom the group consisting of a surfactant, a strong base, apolyelectrolyte, a selectively permeable polymeric barrier, andcombinations thereof. Herein, the phrase “coating reagent coated on thesolid phase material” refers to a material coated on at least a portionof the solid phase material, e.g., on at least a portion of the fibrilmatrix and/or sorptive particles.

Examples of suitable surfactants are listed below.

Examples of suitable strong bases include NaOH, KOH, LiOH, NH₄OH, aswell as primary, secondary, or tertiary amines.

Examples of suitable polyelectrolytes include, polystyrene sulfonic acid(e.g., poly(sodium 4-styrenesulfonate) or PSSA), polyvinyl phosphonicacid, polyvinyl boric acid, polyvinyl sulfonic acid, polyvinyl sulfuricacid, polystyrene phosphonic acid, polyacrylic acid, polymethacrylicacid, lignosulfonate, carrageenan, heparin, chondritin sulfate, andsalts or other derivatives thereof.

Examples of suitable selectively permeable polymeric barriers includepolymers such as acrylates, acryl amides, azlactones, polyvinyl alcohol,polyethylene imine, polysaccharides. Such polymers can be in a varietyof forms. They can be water-soluble, water-swellable, water-insoluble,hydrogels, etc. For example, a polymeric barrier can be prepared suchthat it acts as a filter for larger particles such as white blood cells,nuclei, viruses, bacteria, as well as nucleic acids such as humangenomic DNA and proteins. These surfaces could be tailored by one ofskill in the art to separate on the basis of size and/or charge byappropriate selection of functional groups, by cross-linking, and thelike. Such materials would be readily available or prepared by one ofskill in the art.

Preferably, the solid phase material is coated with a surfactant withoutwashing any surfactant excess away, although the other coating reagentscan be rinsed away if desired. Typically, the coating can be carried outusing a variety of methods such as dipping, rolling, spraying, etc. Thecoating reagent-loaded solid phase material is then typically dried, forexample, in air, prior to use.

Particularly desirable are solid phase materials that are coated with asurfactant, preferably a nonionic surfactant. This can be accomplishedaccording to the procedure set forth in the Examples Section. Althoughnot intending to be limited by theory, the addition of the surfactant isbelieved to increase the wettability of the solid phase material, whichallows the inhibitors to soak into the solid phase material and bindthereto.

The coating reagent for the solid phase materials are preferablyaqueous-based solutions, although organic solvents (alcohols, etc.) canbe used, if desired. The coating reagent loading should be sufficientlyhigh such that the sample is able to wet out the solid phase material.It should not be so high, however, that there is significant elution ofthe coating reagent itself. Preferably, if the coating reagent is elutedwith the nucleic acid, there is no more than about 2 wt-% coatingreagent in the eluted sample. Typically, the coating solutionconcentrations can be as low as 0.1 wt-% coating reagent in the solutionand as high as 10 wt-% coating reagent in the solution.

Surfactants

Nonionic Surfactants. A wide variety of suitable nonionic surfactantsare known that can be used as a lysing reagent (discussed above), aneluting reagent (discussed below), and/or as a coating on the solidphase material. They include, for example, polyoxyethylene surfactants,carboxylic ester surfactants, carboxylic amide surfactants, etc.Commercially available nonionic surfactants include,n-dodecanoylsucrose, n-dodecyl-β-D-glucopyranoside,n-octyl-β-D-maltopyranoside, n-octyl-β-D-thioglucopyranoside,n-decanoylsucrose, n-decyl-β-D-maltopyranoside,n-decyl-β-D-thiomaltoside, n-heptyl-β-D-glucopyranoside,n-heptyl-β-D-thioglucopyranoside, n-hexyl-β-D-glucopyranoside,n-nonyl-β-D-glucopyranoside, n-octanoylsucrose,n-octyl-β-D-glucopyranoside, cyclohexyl-n-hexyl-β-D-maltoside,cyclohexyl-n-methyl-β-D-maltoside, digitonin, and those available underthe trade designations PLURONIC, TRITON, TWEEN, as well as numerousothers commercially available and listed in the Kirk Othmer TechnicalEncyclopedia. Examples are listed in Table 1 below. Preferredsurfactants are the polyoxyethylene surfactants. More preferredsurfactants include octyl phenoxy polyethoxyethanol. TABLE 1 SURFACTANTTRADE NAME NONIONIC SURFACTANT SUPPLIER PLURONIC F127 Modifiedoxyethylated alcohol and/or Sigma oxypropylated straight chain alcoholsSt. Louis, MO TWEEN 20 Polyoxyethylene (20) sorbitan Sigma monolaurateSt. Louis, MO TRITON X-100 t-Octyl phenoxy polyethoxyethanol Sigma St.Louis, MO BRIJ 97 Polyoxyethylene (10) oleyl ether Sigma St. Louis, MOIGEPAL CA-630 Octyl phenoxy poly (ethyleneoxy) Sigma ethanol St. Louis,MO TOMADOL 1-7 Ethoxylated alcohol Tomah Products Milton, WI Vitamin ETPGS d-Alpha tocopheryl polyethylene glycol Eastman 1000 Kingsport, TN

Also suitable are fluorinated nonionic surfactants of the type disclosedin U.S. Pat. Publication Nos. 2003/0139550 (Savu et al.) and2003/0139549 (Savu et al.). Other nonionic fluorinated surfactantsinclude those available under the trade designation ZONYL from DuPont(Wilmington, Del.).

Zwitterionic Surfactants. A wide variety of suitable zwitterionicsurfactants are known that can be used as a coating on the solid phasematerial, as a lysing reagent, and/or as an eluting reagent. Theyinclude, for example, alkylamido betaines and amine oxides thereof,alkyl betaines and amine oxides thereof, sulfo betaines, hydroxy sulfobetaines, amphoglycinates, amphopropionates, balancedamphopolycarboxyglycinates, and alkyl polyaminoglycinates. Proteins havethe ability of being charged or uncharged depending on the pH; thus, atthe right pH, a protein, preferably with a pI of about 8 to 9, such asmodified Bovine Serum Albumin or chymotrypsinogen, could function as azwitterionic surfactant. A specific example of a zwitterionic surfactantis cholamido propyl dimethyl ammonium propanesulfonate available underthe trade designation CHAPS from Sigma. More preferred surfactantsinclude N-dodecyl-N,N dimethyl-3-ammonia-1-propane sulfonate.

Cationic Surfactants. A wide variety of suitable cationic surfactantsare known that can be used as a lysing reagent, an eluting reagent,and/or as a coating on the solid phase material. They include, forexample, quaternary ammonium salts, polyoxyethylene alkylamines, andalkylamine oxides. Typically, suitable quaternary ammonium salts includeat least one higher molecular weight group and two or three lowermolecular weight groups are linked to a common nitrogen atom to producea cation, and wherein the electrically-balancing anion is selected fromthe group consisting of a halide (bromide, chloride, etc.), acetate,nitrite, and lower alkosulfate (methosulfate etc.). The higher molecularweight substituent(s) on the nitrogen is/are often (a) higher alkylgroup(s), containing about 10 to about 20 carbon atoms, and the lowermolecular weight substituents may be lower alkyl of about 1 to about 4carbon atoms, such as methyl or ethyl, which may be substituted, as withhydroxy, in some instances. One or more of the substituents may includean aryl moiety or may be replaced by an aryl, such as benzyl or phenyl.Among the possible lower molecular weight substituents are also loweralkyls of about 1 to about 4 carbon atoms, such as methyl and ethyl,substituted by lower polyalkoxy moieties such as polyoxyethylenemoieties, bearing a hydroxyl end group, and falling within the generalformula:R(CH₂CH₂O)_((n−1))CH₂CH₂OHwhere R is a (C1-C4)divalent alkyl group bonded to the nitrogen, and nrepresents an integer of about 1 to about 15. Alternatively, one or twoof such lower polyalkoxy moieties having terminal hydroxyls may bedirectly bonded to the quaternary nitrogen instead of being bonded to itthrough the previously mentioned lower alkyl. Examples of usefulquaternary ammonium halide surfactants for use in the present inventioninclude but are not limited to methyl-bis(2-hydroxyethyl)coco-ammoniumchloride or oleyl-ammonium chloride, (ETHOQUAD C/12 and O/12,respectively) and methyl polyoxyethylene (15) octadecyl ammoniumchloride (ETHOQUAD 18/25) from Akzo Chemical Inc.

Anionic Surfactants. A wide variety of suitable anionic surfactants areknown that can be used as a lysing reagent, an eluting reagent, and/oras a coating on the solid phase material. Surfactants of the anionictype that are useful include sulfonates and sulfates, such as alkylsulfates, alkylether sulfates, alkyl sulfonates, alkylether sulfonates,alkylbenzene sufonates, alkylbenzene ether sulfates, alkylsulfoacetates,secondary alkane sulfonates, secondary alkylsulfates and the like. Manyof these can include polyalkoxylate groups (e.g., ethylene oxide groupsand/or propylene oxide groups, which can be in a random, sequential, orblock arrangement) and/or cationic counterions such as Na, K, Li,ammonium, a protonated tertiary amine such as triethanolamine or aquaternary ammonium group. Examples include: alkyl ether sulfonates suchas lauryl ether sulfates available under the trade designation POLYSTEPB12 and B22 from Stepan Company, Northfield, Ill., and sodium methyltaurate available under the trade designation NIKKOL CMT30 from NikkoChemicals Co., Tokyo, Japan); secondary alkane sulfonates availableunder the trade designation HOSTAPUR SAS, which is a sodium(C14-C17)secondary alkane sulfonates (alpha-olefin sulfonates), fromClariant Corp., Charlotte, N.C.; methyl-2-sulfoalkyl esters such assodium methyl-2-sulfo(C12-C16)ester and disodium 2-sulfo(C12-C16)fattyacid available from Stepan Company under the trade designation ALPHASTEPC-48; alkylsulfoacetates and alkylsulfosuccinates available as sodiumlaurylsulfoacetate (trade designation LANTHANOL LAL) anddisodiumlaurethsulfosuccinate (trade designation STEPANMILD SL3), bothfrom Stepan Co.; and alkylsulfates such as ammoniumlauryl sulfatecommercially available under the trade designation STEPANOL AM fromStepan Co.

Another class of useful anionic surfactants include phosphates such asalkyl phosphates, alkylether phosphates, aralkylphosphates, andaralkylether phosphates. Many of these can include polyalkoxylate groups(e.g., ethylene oxide groups and/or propylene oxide groups, which can bein a random, sequential, or block arrangement). Examples include amixture of mono-, di- and tri-(alkyltetraglycolether)-o-phosphoric acidesters generally referred to as trilaureth-4-phosphate commerciallyavailable under the trade designation HOSTAPHAT 340KL from ClariantCorp., and PPG-5 ceteth 10 phosphate available under the tradedesignation CRODAPHOS SG from Croda Inc., Parsipanny, N.J., as well asalkyl and alkylamidoalkyldialkylamine oxides. Examples of amine oxidesurfactants include those commercially available under the tradedesignations AMMONYX LO, LMDO, and CO, which are lauryldimethylamineoxide, laurylamidopropyldimethylamine oxide, and cetyl amine oxide, allfrom Stepan Co.

Elution Techniques

For embodiments that use a solid phase material for retaininginhibitors, the more concentrated region of the sample that includesnucleic acid-containing material (e.g., nuclei) and/or released nucleicacid can be eluted using a variety of eluting reagents. Such elutingreagents can include water (preferably RNAse free water), a buffer, asurfactant, which can be cationic, anionic, nonionic, or zwitterionic,or a strong base.

Preferably the eluting reagent is basic (i.e., greater than 7). Forcertain embodiments, the pH of the eluting reagent is at least 8. Forcertain embodiments, the pH of the eluting reagent is up to 10. Forcertain embodiments, the pH of the eluting reagent is up to 13. If theeluted nucleic acid is used directly in an amplification process such asPCR, the eluting reagent should be formulated so that the concentrationof the ingredients will not inhibit the enzymes (e.g., Taq Polymerase)or otherwise prevent the amplification reaction.

Examples of suitable surfactants include those listed above,particularly, those known as SDS, TRITON X-100, TWEEN, fluorinatedsurfactants, and PLURONICS. The surfactants are typically provided inaqueous-based solutions, although organic solvents (alcohols, etc.) canbe used, if desired. The concentration of a surfactant in an elutingreagent is preferably at least 0.1 weight/volume percent (w/v-%), basedon the total weight of the eluting reagent. The concentration of asurfactant in an eluting reagent is preferably no greater than 1 w/v-%,based on the total weight of the eluting reagent. A stabilizer, such aspolyethylene glycol, can optionally be used with a surfactant.

Examples of suitable elution buffers include TRIS-HCl,N-[2-hydroxyethyl]piperazine-N′-[2-ethanesulfonic acid] (HEPES),3-[N-morpholino]propanesulfonic acid (MOPS),piperazine-N,N′-bis[2-ethanesulfonic acid] (PIPES),2-[N-morpholino]ethansulfonic acid (MES), TRIS-EDTA (TE) buffer, sodiumcitrate, ammonium acetate, carbonate salts, and bicarbonates etc.

The concentration of an elution buffer in an eluting reagent ispreferably at least 10 millimolar (mM). The concentration of asurfactant in an eluting reagent is preferably no greater than 2 weightpercent (wt-%).

Typically, elution of the nucleic acid-containing material and/orreleased nucleic acid is preferably accomplished using an alkalinesolution. Although not intending to be bound by theory, it is believedthat an alkaline solution allows for improved binding of inhibitors, ascompared to elution with water. The alkaline solution also facilitateslysis of nucleic acid-containing material. Preferably, the alkalinesolution has a pH of 8 to 13, and more preferably 13. Examples ofsources of high pH include aqueous solutions of NaOH, KOH, LiOH,quaternary nitrogen base hydroxide, tertiary, secondary or primaryamines, etc. If an alkaline solution is used for elution, it istypically neutralized in a subsequent step, for example, with TRISbuffer, to form a PCR-ready sample.

The use of an alkaline solution can selectively destroy RNA, to allowfor the analysis of DNA. Otherwise, RNAse can be added to theformulation to inactivate RNA, followed by heat inactivation of theRNAse. Similarly, DNAse can be added to selectively destroy DNA andallow for the analysis of RNA; however, other lysis buffers (e.g., TE)that do not destroy RNA would be used in such methods. The addition ofRNAse inhibitor such as RNAsin can also be used in a formulation for anRNA preparation that is subjected to real-time PCR.

Elution is typically carried out at room temperature, although highertemperatures may produce higher yields. For example, the temperature ofthe eluting reagent can be up to 95° C. if desired. Elution is typicallycarried out within 10 minutes, although 1-3 minute elution times arepreferred.

Additional Embodiments

In other cases, it may be desirable to isolate various cell typesselectively using known density gradient materials. These densitygradient materials include sucrose and other commercially availableunder the trade designations FICOLL (Amersham Biosciences, Piscataway,N.J.), PERCOLL (Amersham Biosciences, Piscataway, N.J.), HISTOPAQUE(Sigma, St. Louis, Mo.), ISOPREP (Robbins Scientific Corporation,Sunnyvale, Calif.), HISTODENZ (Sigma, St. Louis, Mo.), and OPTIPREP(Sigma, St. Louis, Mo.). The specific cells of interest, for example,peripheral blood mononuclear cells (PBMC's) can be selectively removedby the use of a variable valve device. After extraction of the specificcells of interest, PCR can be directly carried out after lysis as longas the gradient material is PCR compatible. In cases where the gradientmaterial is not PCR compatible, care must be taken to ensure adequatedilution of the sample (e.g., with water or buffer) followed byconcentration of cells and repeating this process a few times to producea PCR ready sample. Alternatively, simply diluting significantly may besufficient to produce a PCR ready sample

For example, in one embodiment of the present invention, a methodincludes: providing a device including a loading chamber and a variablevalved process chamber; placing whole blood in the loading chamber;transferring the whole blood to a valved process chamber; contacting thewhole blood with a density gradient material; centrifuging the wholeblood and density gradient material in the valved process chamber toform layers, at least one of which contains cells of interest; removingat least a portion of the layer containing the cells of interest; andlysing the separated cells of interest to release nucleic acid. In oneaspect of this method, prior to lysing the separated cells of interest,the method includes diluting the separated cells of interest with wateror buffer, optionally further concentrating the diluted layer toincrease the concentration of cells of interest, optionally separatingthe further concentrated region, and optionally repeating this processof dilution followed by concentration and separation. In another aspectof this method, prior to lysing the separated cells of interest, themethod includes diluting the separated cells of interest with water,preferably sufficiently to form a 20×-1000× dilution.

The inhibitors can be removed using solid phase materials, as describedherein (as well as described in U.S. patent application Ser. No. ______,filed on ______, entitled METHODS FOR NUCLEIC ACID ISOLATION AND KITSUSING SOLID PHASE MATERIAL (Attorney Docket No. 59073US003)), prior toor after capture of viral particles onto the beads (for example, asdiscussed below). Such solid phase materials can be used in variousmethods and with various samples described herein.

In addition to this, the level of inhibitors can be reduced usingconcentration/separation/optional dilution steps, for example, asdisclosed in U.S. patent application Ser. No. ______, filed on ______,entitled METHODS FOR NUCLEIC ACID ISOLATION AND KITS USING AMICROFLUIDIC DEVICE AND CONCENTRATION STEP (Attorney Docket No.59801US002).

In other embodiments, it may be necessary to capture viral DNA/RNA inthe white blood cell. In these cases, the white blood cells can beisolated using a variable valve and beads can be used to capture theviral DNA/RNA.

For example, beads can be functionalized with the appropriate groups toisolate specific cells, viruses, bacteria, proteins, nucleic acids, etc.The beads can be segregated from the sample by centrifugation andsubsequent separation. The beads could be designed to have theappropriate density and sizes (nanometers to microns) for segregation.For example, in the case of viral capture, beads that recognize theprotein coat of a virus can be used to capture and concentrate the virusprior to or after removal of small amounts of residual inhibitors from aserum sample.

Nucleic acids can be extracted out of the segregated viral particles bylysis. Thus, the beads could provide a way of concentrating relevantmaterial in a specific region within a device, also allowing for washingof irrelevant materials and elution of relevant material from thecaptured particle.

Examples of such beads include, but are not limited to, crosslinkedpolystyrene beads available under the trade designation CHELEX fromBio-Rad Laboratories, Inc. (Hercules, Calif.), crosslinked agarose beadswith tris(2-aminoethyl)amine, iminodiacetic acid, nitrilotriacetic acid,polyamines and polyimines as well as the chelating ion exchange resinscommercially available under the trade designation DUOLITE C-467 andDUOLITE GT73 from Rohm and Haas (Philadelphia, Pa.), AMBERLITE IRC-748,DIAION CR11, DUOLITE C647. These beads are also suitable for use as thesolid phase material as discussed above.

Other examples of beads include those available under the tradedesignations GENE FIZZ (Eurobio, France), GENE RELEASER (BioventuresInc., Murfreesboro, Tenn.), and BUGS N BEADS (GenPoint, Oslo, Norway),as well as Zymo's beads (Zymo Research, Orange, Calif.) and DYNAL beads(Dynal, Oslo, Norway).

Other materials are also available for pathogen capture. For example,polymer coatings can also be used to isolate specific cells, viruses,bacteria, proteins, nucleic acids, etc. in certain embodiments of theinvention. These polymer coatings could directly be spray-jetted, forexample, onto the cover film of a device.

Viral particles can be captured onto beads by covalently attachingantibodies onto bead surfaces. The antibodies can be raised against theviral coat proteins. For example, DYNAL beads can be used to covalentlylink antibodies. Alternatively, synthetic polymers, for example,anion-exchange polymers, can be used to concentrate viral particles.Commercially available resins such as viraffinity (Biotech SupportGroup, East Brunswick, N.J.) can be used to coat beads or applied aspolymer coatings onto select locations in a device to concentrate viralparticles. BUGS N BEADS (GenPoint, Oslo, Norway) can, for example, beused for extraction of bacteria. Here, these beads can be used tocapture bacteria such as Staphylococcus, Streptococcus, E coli,Salmonella, and Clamydia elementary bodies.

Thus, in one embodiment of the present invention when the sampleincludes viral particles or other pathogens (e.g., bacteria), a devicecan include solid phase material in the form of viral capture beads orother pathogen capture material. In this method, the sample contacts theviral capture beads. More specifically, in one case, the viral capturebeads can be used only for concentration of virus or bacteria, forexample, followed by segregation of beads to another chamber, endingwith lysis of virus or bacteria. In another case, the beads can be usedfor concentration of virus or bacteria, followed by lysis and capture ofnucleic acids onto the same bead, dilution of beads, concentration ofbeads, segregation of beads, and repeating the process multiple timesprior to elution of captured nucleic acid.

In a specific embodiment, a method includes: providing a deviceincluding a loading chamber, a variable valved process chamber, and aseparation chamber including pathogen capture material; placing wholeblood in the loading chamber; transferring the whole blood to a valvedprocess chamber; centrifuging the whole blood in the valved processchamber to form a plasma layer including one or more pathogens, a redblood cell layer, and an interfacial layer (therebetween) includingwhite blood cells; transferring at least a portion of the plasma layerincluding the one or more pathogens to the separation chamber havingpathogen capture material therein; separating at least a portion of theone or more pathogens from the pathogen capture material; and lysing theone or more pathogens to release nucleic acid.

Alternatively, if beads (or other pathogen capture material) are not themethod of choice for viral capture (or other pathogen capture), then onemay choose to pellet out viral particles from serum or plasma using anultracentrifuge. These concentrated viral particles can be transferredto the device for lysing with a surfactant with the addition of an RNAseinhibitor, for example, if viral RNA needs to be isolated followed by anamplification reaction (RT-PCR).

If the downstream application of the nucleic acid is subjecting it to anamplification process such as PCR, then all reagents used in the methodare preferably compatible with such process (e.g., PCR compatible).Furthermore, the addition of PCR facilitators may be useful, especiallyfor diagnostic purposes. Also, heating of the material to be amplifiedprior to amplification can be beneficial.

In embodiments in which the inhibitors are not completely removed, theuse of buffers, enzymes, and PCR facilitators can be added that help inthe amplification process in the presence of inhibitors. For example,enzymes other than Taq Polymerase, such as rTth, that are more resistantto inhibitors can be used, thereby providing a huge benefit for PCRamplification. The addition of Bovine Serum Albumin, betaine, proteinaseinhibitors, bovine transferrin, etc. can be used as they are known tohelp even further in the amplification process. Alternatively, one canuse a commercially available product such as Novagen's Blood Direct PCRBuffer kit (EMD Biosciences, Darmstadt, Germany) for directamplification from whole blood without the need for extensivepurification.

Objects and advantages of this invention may be further illustrated bythe following examples, but the particular materials and amounts thereofrecited in these examples, as well as other conditions and details,should not be construed to unduly limit this invention.

EXAMPLES Example 1 Preparation of Solid Phase Material: Ammonia Formwith TRITON-X 100

A 3M No. 2271 EMPORE Extraction Chelating Disk was placed in a glassfilter holder. The extraction disk was converted into the ammonia form,following the procedure printed on the package insert. The disk placedin a vial and was submerged in a 1% TRITON-X 100 (Sigma-Aldrich, St.Louis, Mo.) solution (0.1 gram (g) of TRITON-X 100 in 10 mL of water),mixing for about 6-8 hours on a Thermolyne Vari-Mix Model M48725 Rocker(Barnstead/Thermolyne, Dubuque, Iowa). The disk was placed in glassfilter holder, dried by applying a vacuum for about 20 minutes (min),and then dried overnight at room temperature (approximately 21° C.),taking care not to wash or rinse the disk.

Example 2A Effect of Inhibitor/DNA on PCR: Varying InhibitorConcentration with Fixed DNA Concentration

A dilution series of inhibitors were made prior to spiking with cleanhuman genomic DNA in order to study the effect of inhibitor on PCR. To10 μL of 15 nanograms per microliter (ng/μL) human genomic DNA, 1μL ofdifferent Mix I (neat or dilutions thereof) was added (Samples 2—noinhibitor added, 2D—neat, 2E—1:10, 2F—1:30, 2G—1:100, 2H—1:300) andvortexed. Two (2) μL aliquots of each sample were taken for 20 μL PCR.The results are shown in Table 2.

Mix I: one hundred (100) μL of whole blood was added to 1 μL of neatTRITON-X 100. The solution was incubated at room temperature(approximately 21° C.) for about 5 minutes, vortexing the solutionintermittently (for approximately 5 seconds every 20 seconds). Thesolution was investigated to make sure that it was transparent beforeproceeding to the next step. The solution was spun in an Eppendorf Model5415D centrifuge at 400 rcf for about 10 minutes. Approximately 80 μLfrom the top of the microcentrifuge tube and designated Mix I.

Example 2B Effect of Inhibitor/DNA on PCR: Varying DNA Concentrationwith Fixed Inhibitor Concentration

To 10 μL of human genomic DNA, 1 μL of 1:3 diluted Mix I (describedabove) was added. DNA concentrations that were examined were thefollowing: Samples 2J—15 ng/μL, 2K—7.5 ng/μL, 2L—3.75 ng/μL, 2M—1.5ng/μL. Two (2) μL aliquots of each sample were taken for 20 μL PCR. Theresults are shown in Table 2.

Example 2C Effect of Inhibitor/DNA on PCR: DNA with No Added Inhibitor

The following samples were prepared with 1 μL of water added to each DNAsample instead of inhibitor: Samples 2N—15 ng/μL, 2P—7.5 ng/μL, 2Q—3.75ng/μL, 2R—1.5 ng/μL. Two (2) μL aliquots of each sample were taken for20 μL PCR. The results are shown in Table 2. TABLE 2 Ct (duplicateSample No. samples) 2 19.10 19.06 2D 13.94 29.50 2E 27.39 26.22 2F 21.4420.66 2G 19.90 19.30 2H 19.90 20.08 2J 28.45 28.61 2K 29.16 30.22 2L30.47 29.96 2M 28.43 26.16 2N 20.05 19.80 2P 20.74 20.54 2Q 21.95 21.882R 22.67 23.10

Example 3 Procedure for Isolation of Genomic DNA from Whole Blood withthe Use of a Chelating Solid Phase Material

Six hundred (600) μL of whole blood was spun at 2500 rpm for 10 min. Thesupernatant was separated and discarded, and the buffy coat wasextracted from the interfacial layer. Five (5) μL of buffy coat wasadded to five (5) μL of 2% TRITON-X. The solution was mixed thoroughly,and placed onto a 3M No. 2271 EMPORE Extraction Chelating Disk preparedas described in Example 1 using 10% TRITON-X 100 instead of 1% TRITON-X100 as a loading solution. After the solution had soaked into the disk,the sample was extracted with a twenty (20) μL aliquot of 0.1M NaOH. Thesolution was briefly spun in an Eppendorf Model 5415D centrifuge at 400rcf. An aliquot of eleven (11) μL of sample was heated for 3 min at 95°C., and then added to three (3) μL of 1 M TRIS-HCl (pH 7.4).

Example 4 Procedure for Isolation of Genomic DNA from Whole Blood

Six hundred (600) μL of whole blood was spun at 2500 rpm for 10 min. Thesupernatant was separated and discarded, and the buffy coat wasextracted from the interfacial layer. Five (5) μL of buffy coat wasadded to the ninety five (95) μL of RNase-free sterile water. Thesolution was mixed until the color became uniform and spun in anEppendorf Model 5415D centrifuge at 400 rcf for about 2 minutes. Analiquot of ninety five (95) μL of the solution from the top wasseparated and discarded, leaving about five (5) μL of concentratedmaterial at the bottom of the centrifuge tube. To the last 5 μL ofconcentrated material, 95 μL of RNase-free sterile water was added. Thesample was mixed until the color became uniform. The solution was spunin an Eppendorf Model 5415D centrifuge at 400 rcf for about 2 minutes. A95 μL of the solution on the top was separated and discarded, leavingabout ten (10) μL of concentrated material at the bottom of thecentrifuge tube. To the last 10 μL of concentrated material, one (1) μLof 1 M NaOH was added. After 1 min incubation, the sample was heated for3 min at 95° C. A 3 μL of 1 M TRIS-HCl (pH 7.4) was added to 11 μL ofsample.

Results

Table 3 reports results that were obtained on ABI 7700 QPCR Machine(Applera, Foster City, Calif.) following the instructions in QuantiTechSYBR Green PCR Handbook on p. 10-12 for preparation of a 10 μL PCRsample (2 μL of sample in 10 μL SYBR Green Master Mix, 4 μL β-actin, 4μL of water) for Examples 1-2; Results for Examples 3-4 were obtained onLightCycler 2.0 (Roche Applied Science, Indianapolis, Ind.) followingthe instructions in LightCycler Factor V Leiden Mutation Kit's packageinsert on p. 2-3 for preparation of a 10 μL PCR sample (2.5 μL of samplein 5.5 μL of RNase-free sterile water, 1 μL of 10× Factor V LeidenReaction Mix and 1 μL of 10× Factor V Leiden Mutation Detection Mix).Spectra measurements were run on a SpectraMax Plus³⁸⁴ spectrophotometerat 405 nm (Molecular Devices Corporation, Sunnyvale, Calif.). Two, threeor four values for each sample represent duplicates, triplicates, orquadruplicates. TABLE 3 405 nm Samples Ct (avg) 1.5 ng/μL human genomic16.92 — DNA in 0.1 M NaOH/40 mM 20.67 TRIS-HCl buffer 1.5 ng/μL humangenomic 19.01 0 DNA in water 18.67 1.5 ng/μL human genomic 16.18 — DNAin water 16.28 Examples 2A and 2B Mix I — 2.63 diluted 1:36 Examples 2Aand 2B — 0.38 Mix I diluted 1:360 Examples 2A and 2B — 0.036 Mix Idiluted 1:3600 Examples 2A and 2B — 0 Mix I diluted 1:36000 Example 3*26.02, 24.93 — Example 4* 22.73, 23.93 —*Positive Control for Examples 3-4 was DNA extracted from two hundred(200) μL of whole blood following “Blood and Body Fluid Spin Protocol”described in QIAamp DNABlood Mini Kit Handbook p. 27, eluting in 200 μL of water and had Ctvalue of 20-21. Negative Control (NTC or no template control) did notamplify in these experiments.

As used herein and in the appended claims, the singular forms “a,”“and,” and “the” include plural referents unless the context clearlydictates otherwise. Thus, for example, reference to “a valve lip”includes a plurality of valve lips and reference to “the processchamber” includes reference to one or more process chambers andequivalents thereof known to those skilled in the art.

All references and publications cited herein are expressly incorporatedherein by reference in their entirety into this disclosure. Illustrativeembodiments of this invention are discussed and reference has been madeto possible variations within the scope of this invention. These andother variations and modifications in the invention will be apparent tothose skilled in the art without departing from the scope of theinvention, and it should be understood that this invention is notlimited to the illustrative embodiments set forth herein. Accordingly,the invention is to be limited only by the claims provided below andequivalents thereof.

1. A valved process chamber on a sample processing device, the valvedprocess chamber comprising: a process chamber comprising a processchamber volume located between opposing first and second major sides ofthe sample processing device, wherein the process chamber occupies aprocess chamber area on the sample processing device, and wherein theprocess chamber area comprises a length and a width transverse to thelength, and further wherein the length is greater than the width; avalve chamber located within the process chamber area, the valve chamberlocated between the process chamber volume and the second major side ofthe sample processing device, wherein the valve chamber is isolated fromthe process chamber by a valve septum separating the valve chamber andthe process chamber, and wherein a portion of the process chamber volumelies between the valve septum and a first major side of the sampleprocessing device; and a detection window located within the processchamber area, wherein the detection window is transmissive to selectedelectromagnetic energy directed into and/or out of the process chambervolume.
 2. A valved process chamber according to claim 1, wherein thedetection window is coextensive along the length of the process chamberwith the valve septum.
 3. A valved process chamber according to claim 1,wherein the detection window is formed through the first major side ofthe sample processing device.
 4. A valved process chamber according toclaim 1, wherein the detection window is formed through the second majorside of the sample processing device.
 5. A valved process chamberaccording to claim 1, wherein the valve chamber and the detection windowoccupy mutually exclusive portions of the process chamber area.
 6. Avalved process chamber according to claim 1, wherein the detectionwindow is formed through the second major side of the sample processingdevice, and wherein the valve chamber and the detection window occupymutually exclusive portions of the process chamber area.
 7. A valvedprocess chamber according to claim 1, wherein the valve septum extendsalong the length of the process chamber area for 30% or more of amaximum length of the process chamber area.
 8. A valved process chamberaccording to claim 1, wherein the valve septum extends for a length of 1millimeter or more along the length of the process chamber.
 9. A valvedprocess chamber according to claim 1, wherein the sample processingdevice is opaque between the process chamber volume and the first majorside of the sample processing device.
 10. A valved process chamberaccording to claim 1, wherein at least a portion of the valve chamber islocated within a valve lip extending into the process chamber area, andwherein the valve septum is formed in the valve lip.
 11. A valvedprocess chamber according to claim 10, wherein the valve lip occupiesonly a portion of the width of the process chamber area.
 12. A valvedprocess chamber according to claim 11, wherein the detection windowoccupies at least a portion of the width of the process chamber areathat is not occupied by the valve lip.
 13. A valved process chamber on asample processing device, the valved process chamber comprising: aprocess chamber comprising a process chamber volume located betweenopposing first and second major sides of the sample processing device,wherein the process chamber occupies a process chamber area on thesample processing device, and wherein the process chamber area comprisesa length and a width transverse to the length, and further wherein thelength is greater than the width; a valve chamber located within theprocess chamber area, the valve chamber located between the processchamber volume and the second major side of the sample processingdevice, wherein the valve chamber is isolated from the process chamberby a valve septum separating the valve chamber and the process chamber,and wherein a portion of the process chamber volume lies between thevalve septum and a first major side of the sample processing device, andfurther wherein the valve chamber and the detection window occupymutually exclusive portions of the process chamber area, and stillfurther wherein at least a portion of the valve chamber is locatedwithin a valve lip extending into the process chamber area, and whereinthe valve septum is formed in the valve lip; and a detection windowlocated within the process chamber area, wherein the detection window istransmissive to selected electromagnetic energy directed into and/or outof the process chamber volume.
 14. A method of selectively removingsample material from a process chamber, the method comprising: providinga sample processing device comprising: a process chamber comprising aprocess chamber volume, wherein the process chamber occupies a processchamber area on the sample processing device, and wherein the processchamber area comprises a length and a width transverse to the length,and further wherein the length is greater than the width; a valvechamber located within the process chamber area, wherein the valvechamber is isolated from the process chamber by a valve septum locatedbetween the valve chamber and the process chamber; and a detectionwindow located within the process chamber area, wherein the detectionwindow is transmissive for selected electromagnetic energy; providingsample material in the process chamber; detecting a characteristic ofthe sample material in the process chamber through the detection window;forming an opening in the valve septum at a selected location along thelength of the process chamber, wherein the selected location iscorrelated to the detected characteristic of the sample material; andmoving only a portion of the sample material from the process chamberinto the valve chamber through the opening formed in the valve septum.15. A method according to claim 14, wherein moving only a portion of thesample material from the process chamber into the valve chambercomprises rotating the sample processing device.
 16. A method accordingto claim 14, wherein the process chamber area comprises a length and awidth transverse to the length, and further wherein the length isgreater than the width.
 17. A method according to claim 14, wherein thedetected characteristic comprises a free surface of the sample material,and wherein the portion of the sample material moved from the processchamber into the valve chamber comprises a selected volume of the samplematerial.
 18. A method according to claim 14, further comprisingrotating the sample processing device to separate components of thesample material in the process chamber.
 19. A method according to claim18, wherein the detected characteristic of the sample material comprisesa boundary between the separated components of the sample material, andwherein the portion of the sample material moved from the processchamber into the valve chamber comprises a portion of a selectedcomponent of the sample material.
 20. A method according to claim 14,wherein moving only a portion of the sample material from the processchamber into the valve chamber comprises moving a selected volume of thesample material from the process chamber into the valve chamber.
 21. Amethod according to claim 14, wherein the sample material comprisesblood.
 22. A method of selectively removing sample material from aprocess chamber, the method comprising: providing a sample processingdevice comprising: a process chamber comprising a process chambervolume, wherein the process chamber occupies a process chamber area onthe sample processing device, and wherein the process chamber areacomprises a length and a width transverse to the length, and furtherwherein the length is greater than the width; a valve chamber locatedwithin the process chamber area, wherein the valve chamber is isolatedfrom the process chamber by a valve septum located between the valvechamber and the process chamber; and a detection window located withinthe process chamber area, wherein the detection window is transmissivefor selected electromagnetic energy; providing sample material in theprocess chamber; detecting a characteristic of the sample material inthe process chamber through the detection window; forming an opening inthe valve septum at a selected location within the process chamber area,wherein the selected location is correlated to the detectedcharacteristic of the sample material; and moving only a portion of thesample material from the process chamber into the valve chamber throughthe opening formed in the valve septum by rotating the sample processingdevice.
 23. A method of isolating nucleic acid from whole blood, themethod comprising: providing a device comprising a loading chamber and avariable valved process chamber; placing whole blood in the loadingchamber; transferring the whole blood to a valved process chamber;centrifuging the whole blood in the valved process chamber to form aplasma layer, a red blood cell layer, and an interfacial layercomprising white blood cells; removing at least a portion of theinterfacial layer comprising white blood cells; and lysing the whiteblood cells in the separated interfacial layer and optionally lysing thenuclei therein to release inhibitors and/or nucleic acid.
 24. The methodof claim 23 wherein prior to lysing the white blood cells, the methodincludes diluting the separated interfacial layer of the sample withwater or buffer, optionally further concentrating the diluted layer toincrease the concentration of nucleic acid material, optionallyseparating the further concentrated region, and optionally repeatingthis process of dilution followed by concentration and separation toreduce the inhibitor concentration to that which would not interferewith an amplification method.
 25. The method of claim 23 wherein thedevice further comprises a separation chamber comprising a solid phasematerial.
 26. The method of claim 25 wherein the solid phase materialcomprises capture sites, a coating reagent coated on the solid phasematerial, or both; wherein the coating reagent is selected from thegroup consisting of a surfactant, a strong base, a polyelectrolyte, aselectively permeable polymeric barrier, and combinations thereof. 27.The method of claim 25 further comprising contacting the lysed samplewith the solid phase material in the separation chamber topreferentially adhere at least a portion of the inhibitors to the solidphase material; wherein lysing can occur before, simultaneous with, orafter contacting the solid phase material.
 28. The method of claim 25further comprising separating at least a portion of the nuclei and/ornucleic acid from the solid phase material having at least a portion ofthe inhibitors adhered thereto.
 29. The method of claim 23 whereinlysing comprises subjecting the white blood cells to a strong base withoptional heating to release nucleic acid.
 30. The method of claim 29further comprising adjusting the pH of the sample comprising thereleased nucleic acid to be within a range of 7.5 to
 9. 31. The methodof claim 23 further comprising diluting the lysed sample with water toreduce the inhibitor concentration to that which would not interferewith an amplification method; optionally further lysing the nuclei torelease nucleic acid; and optionally adjusting the pH of the samplecomprising released nucleic acid.
 32. The method of claim 31 whereindiluting the lysed sample comprises diluting with water to reduce theconcentration of heme to less than 2 micromolar.
 33. The method of claim31 wherein diluting the lysed sample comprises diluting sufficientlywith water to form a 20×-1000× dilution of the lysed sample.
 34. Themethod of claim 31 wherein the water is RNAse-free sterile water.
 35. Amethod of isolating nucleic acid from whole blood, the methodcomprising: providing a device comprising a loading chamber and avariable valved process chamber; placing whole blood in the loadingchamber; transferring the whole blood to a valved process chamber;contacting the whole blood with a density gradient material;centrifuging the whole blood and density gradient material in the valvedprocess chamber to form layers, at least one of which contains cells ofinterest; removing at least a portion of the layer comprising the cellsof interest; and lysing the separated cells of interest to releasenucleic acid.
 36. The method of claim 35 wherein prior to lysing theseparated cells of interest, the method includes diluting the separatedcells of interest with water or buffer, optionally further concentratingthe diluted layer to increase the concentration of cells of interest,optionally separating the further concentrated region, and optionallyrepeating this process of dilution followed by concentration andseparation.
 37. The method of claim 35 wherein prior to lysing theseparated cells of interest, the method includes diluting the separatedcells of interest with water.
 38. The method of claim 37 whereindiluting the separated cells of interest comprises diluting sufficientlywith water to form a 20×-1000× dilution.
 39. A method of isolatingnucleic acid from whole blood comprising one or more pathogens, themethod comprising: providing a device comprising a loading chamber, avariable valved process chamber, and a separation chamber comprisingpathogen capture material; placing whole blood in the loading chamber;transferring the whole blood to a valved process chamber; centrifugingthe whole blood in the valved process chamber to form a plasma layercomprising one or more pathogens, a red blood cell layer, and aninterfacial layer comprising white blood cells; transferring at least aportion of the plasma layer comprising one or more pathogens to theseparation chamber comprising pathogen capture material; separating atleast a portion of the one or more pathogens from the pathogen capturematerial; and lysing the one or more pathogens to release nucleic acid.40. A kit for isolating nucleic acid from a sample, the kit comprising:a device comprising a loading chamber and a variable valved processchamber; and instructions for centrifuging whole blood and removing aportion of the whole blood according to the method of claim 23.